TheSeed - User contributions [en]

SEED Viewer Manual

2008-12-15T17:10:44Z

DanielaBartels: /* (3) Login Box */

The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions.

These pages will cover the usage of the different pages within the Seed Viewer.

An overview of the main pages in the SeedViewer can be found in the '''[[SEED_Viewer_Manual/Contents|Contents Page]]'''.

== Home ==

The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]].

Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components:

=== (1) [[SEED_Viewer_Manual/Menu|The menu]] ===

The menu is a green bar located under the SeedViewer Logo.
Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''[[SEED_Viewer_Manual/Menu#Navigate_Menu|Navigate]]''' and '''[[SEED_Viewer_Manual/Menu#Help_Menu|Help]]''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu.

=== (2) [[SEED_Viewer_Manual/Find|Find Window]] ===

On the right side of the menu bar you will find an input field with a '''find''' button in front of it.
The Find Window allows you to search the SEED data for keywords or ids. To learn more about the search using the Find Window, click [[SEED_Viewer_Manual/Find|here]].

=== (3) [[WebComponents/Login|Login Box]] ===

For using the publicly available data in the SEED no login or registration is required. If you wish to use our services [[RAST_Tutorial|RAST]] or [[MG_RAST_Tutorial|MG-RAST]], you need to obtain a login. That way, we can ensure that only you have access to your private data. This is also very helpfull for feedback and support.

You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]].

=== (4) Body of the Page ===

The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|TabView]] at the bottom of the Home page:

'''a) Organisms'''

Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism.

'''b) Subsystems'''

Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box.

'''c) ID search'''

If you know the ID of a gene or protein you're interested in, you can directly specify it in this field and press '''ID Search'''. The ID can be a SEED (fig|...) ID as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Glossary#Aliases|Aliases]].

'''d) Text search'''

You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as [[Glossary#Functional role|Functional Roles]] of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab.

'''e) BLAST'''

This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]].

[[Image:Home1.png]]

AnnotationClearingHouse

2008-12-15T11:55:35Z

DanielaBartels:

== Annotation Clearing House ==

SEED Viewer Manual

2008-12-15T11:37:43Z

DanielaBartels: /* (4) Body of the Page */

The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions.

These pages will cover the usage of the different pages within the Seed Viewer.

An overview of the main pages in the SeedViewer can be found in the '''[[SEED_Viewer_Manual/Contents|Contents Page]]'''.

== Home ==

The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]].

Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components:

=== (1) [[SEED_Viewer_Manual/Menu|The menu]] ===

The menu is a green bar located under the SeedViewer Logo.
Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''[[SEED_Viewer_Manual/Menu#Navigate_Menu|Navigate]]''' and '''[[SEED_Viewer_Manual/Menu#Help_Menu|Help]]''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu.

=== (2) [[SEED_Viewer_Manual/Find|Find Window]] ===

On the right side of the menu bar you will find an input field with a '''find''' button in front of it.
The Find Window allows you to search the SEED data for keywords or ids. To learn more about the search using the Find Window, click [[SEED_Viewer_Manual/Find|here]].

=== (3) [[WebComponents/Login|Login Box]] ===

Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]].

=== (4) Body of the Page ===

The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|TabView]] at the bottom of the Home page:

'''a) Organisms'''

Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism.

'''b) Subsystems'''

Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box.

'''c) ID search'''

If you know the ID of a gene or protein you're interested in, you can directly specify it in this field and press '''ID Search'''. The ID can be a SEED (fig|...) ID as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Glossary#Aliases|Aliases]].

'''d) Text search'''

You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as [[Glossary#Functional role|Functional Roles]] of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab.

'''e) BLAST'''

This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]].

[[Image:Home1.png]]

SEED Viewer Manual

2008-12-15T11:37:08Z

DanielaBartels: /* (4) Body of the Page */

The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions.

These pages will cover the usage of the different pages within the Seed Viewer.

An overview of the main pages in the SeedViewer can be found in the '''[[SEED_Viewer_Manual/Contents|Contents Page]]'''.

== Home ==

The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]].

Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components:

=== (1) [[SEED_Viewer_Manual/Menu|The menu]] ===

The menu is a green bar located under the SeedViewer Logo.
Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''[[SEED_Viewer_Manual/Menu#Navigate_Menu|Navigate]]''' and '''[[SEED_Viewer_Manual/Menu#Help_Menu|Help]]''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu.

=== (2) [[SEED_Viewer_Manual/Find|Find Window]] ===

On the right side of the menu bar you will find an input field with a '''find''' button in front of it.
The Find Window allows you to search the SEED data for keywords or ids. To learn more about the search using the Find Window, click [[SEED_Viewer_Manual/Find|here]].

=== (3) [[WebComponents/Login|Login Box]] ===

Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]].

=== (4) Body of the Page ===

The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|TabView]] at the bottom of the Home page:

'''a) Organisms'''

Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism.

'''b) Subsystems'''

Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box.

'''c) ID search'''

If you know the ID of a gene or protein you're interested in, you can directly specify it in this field and press '''ID Search'''. The ID can be a SEED (fig|...) ID as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Glossary#Aliases|Aliases]].

'''d) Text search'''

You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as [[Glossary#Functional Role|Functional Roles]] of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab.

'''e) BLAST'''

This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]].

[[Image:Home1.png]]

SEED Viewer Manual

2008-12-15T11:36:51Z

DanielaBartels: /* (4) Body of the Page */

The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions.

These pages will cover the usage of the different pages within the Seed Viewer.

An overview of the main pages in the SeedViewer can be found in the '''[[SEED_Viewer_Manual/Contents|Contents Page]]'''.

== Home ==

The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]].

Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components:

=== (1) [[SEED_Viewer_Manual/Menu|The menu]] ===

The menu is a green bar located under the SeedViewer Logo.
Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''[[SEED_Viewer_Manual/Menu#Navigate_Menu|Navigate]]''' and '''[[SEED_Viewer_Manual/Menu#Help_Menu|Help]]''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu.

=== (2) [[SEED_Viewer_Manual/Find|Find Window]] ===

On the right side of the menu bar you will find an input field with a '''find''' button in front of it.
The Find Window allows you to search the SEED data for keywords or ids. To learn more about the search using the Find Window, click [[SEED_Viewer_Manual/Find|here]].

=== (3) [[WebComponents/Login|Login Box]] ===

Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]].

=== (4) Body of the Page ===

The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|TabView]] at the bottom of the Home page:

'''a) Organisms'''

Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism.

'''b) Subsystems'''

Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box.

'''c) ID search'''

If you know the ID of a gene or protein you're interested in, you can directly specify it in this field and press '''ID Search'''. The ID can be a SEED (fig|...) ID as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Glossary#Aliases|Aliases]].

'''d) Text search'''

You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as [[Glossary|Functional Role|Functional Roles]] of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab.

'''e) BLAST'''

This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]].

[[Image:Home1.png]]

SEED Viewer Manual

2008-12-15T11:34:04Z

DanielaBartels: /* (2) Find Window */

The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions.

These pages will cover the usage of the different pages within the Seed Viewer.

An overview of the main pages in the SeedViewer can be found in the '''[[SEED_Viewer_Manual/Contents|Contents Page]]'''.

== Home ==

The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]].

Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components:

=== (1) [[SEED_Viewer_Manual/Menu|The menu]] ===

The menu is a green bar located under the SeedViewer Logo.
Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''[[SEED_Viewer_Manual/Menu#Navigate_Menu|Navigate]]''' and '''[[SEED_Viewer_Manual/Menu#Help_Menu|Help]]''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu.

=== (2) [[SEED_Viewer_Manual/Find|Find Window]] ===

On the right side of the menu bar you will find an input field with a '''find''' button in front of it.
The Find Window allows you to search the SEED data for keywords or ids. To learn more about the search using the Find Window, click [[SEED_Viewer_Manual/Find|here]].

=== (3) [[WebComponents/Login|Login Box]] ===

Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]].

=== (4) Body of the Page ===

The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|TabView]] at the bottom of the Home page:

'''a) Organisms'''

Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism.

'''b) Subsystems'''

Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box.

'''c) ID search'''

If you know the ID of a gene or protein you're interested in, you can directly type it into this field and press '''ID Search'''. The ID can be a SEED (fig) id as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Glossary#Aliases|Aliases]].

'''d) Text search'''

You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as Functional Roles of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab.

'''e) BLAST'''

This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]].

[[Image:Home1.png]]

SEED Viewer Manual

2008-12-15T11:33:06Z

DanielaBartels: /* (2) Find Window */

The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions.

These pages will cover the usage of the different pages within the Seed Viewer.

An overview of the main pages in the SeedViewer can be found in the '''[[SEED_Viewer_Manual/Contents|Contents Page]]'''.

== Home ==

The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]].

Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components:

=== (1) [[SEED_Viewer_Manual/Menu|The menu]] ===

The menu is a green bar located under the SeedViewer Logo.
Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''[[SEED_Viewer_Manual/Menu#Navigate_Menu|Navigate]]''' and '''[[SEED_Viewer_Manual/Menu#Help_Menu|Help]]''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu.

=== (2) [[SEED_Viewer_Manual/Find|Find Window]] ===

On the right side of the menu bar you will find an input field labeled '''Find'''.
The Find Window allows you to search the SEED data for keywords or ids. To learn more about the Find Window, click [[SEED_Viewer_Manual/Find|here]].

=== (3) [[WebComponents/Login|Login Box]] ===

Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]].

=== (4) Body of the Page ===

The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|TabView]] at the bottom of the Home page:

'''a) Organisms'''

Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism.

'''b) Subsystems'''

Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box.

'''c) ID search'''

If you know the ID of a gene or protein you're interested in, you can directly type it into this field and press '''ID Search'''. The ID can be a SEED (fig) id as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Glossary#Aliases|Aliases]].

'''d) Text search'''

You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as Functional Roles of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab.

'''e) BLAST'''

This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]].

[[Image:Home1.png]]

SEED Viewer Manual

2008-12-15T11:30:46Z

DanielaBartels: /* (1) The menu */

The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions.

These pages will cover the usage of the different pages within the Seed Viewer.

An overview of the main pages in the SeedViewer can be found in the '''[[SEED_Viewer_Manual/Contents|Contents Page]]'''.

== Home ==

The home page of the seedviewer offers you several entry points to explore the data in the [[Home_of_the_SEED|SEED]].

Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components:

=== (1) [[SEED_Viewer_Manual/Menu|The menu]] ===

The menu is a green bar located under the SeedViewer Logo.
Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories '''[[SEED_Viewer_Manual/Menu#Navigate_Menu|Navigate]]''' and '''[[SEED_Viewer_Manual/Menu#Help_Menu|Help]]''' will always be present on each page. Other menu categories are added dependent on the context of the page. Click [[SEED_Viewer_Manual/Menu|here]] to learn more about using the menu.

=== (2) [[SEED_Viewer_Manual/Find|Find Window]] ===

The Find window allows you to search for keywords or ids. To learn more about the find window, click [[SEED_Viewer_Manual/Find|here]].

=== (3) [[WebComponents/Login|Login Box]] ===

Some actions may require a user to get a user account and log in. This is necessary for viewing private organisms a user has uploaded to the [[RAST_Tutorial|RAST]]. You can create a login by clicking on '''Register''' in the '''Help''' menu. To learn more about user management click [[SEED_Viewer_Manual/UserManagement|here]].

=== (4) Body of the Page ===

The home page allows you to specifically search the SEED data using five categories. They are presented in a [[WebComponents/Tabview|TabView]] at the bottom of the Home page:

'''a) Organisms'''

Select an organism of interest in the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] and press the button '''select'''. This will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of that organism.

'''b) Subsystems'''

Selecting a subsystem in the Select Box and clicking '''Select''' will lead you to a [[SEED_Viewer_Manual/Subsystems|Subsystem Page]]. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box.

'''c) ID search'''

If you know the ID of a gene or protein you're interested in, you can directly type it into this field and press '''ID Search'''. The ID can be a SEED (fig) id as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as [[Glossary#Aliases|Aliases]].

'''d) Text search'''

You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as Functional Roles of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab.

'''e) BLAST'''

This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail [[SEED_Viewer_Manual/BLASTOrganism|here]].

[[Image:Home1.png]]

File:SeedViewerOverview.png

2008-12-12T15:04:36Z

DanielaBartels:

SEED Viewer Manual/Contents

2008-12-12T15:02:52Z

DanielaBartels: /* Main pages of the SeedViewer */

== Overview of the pages in the SeedViewer ==

[[Image:SeedViewerOverview.png]]

== Main pages of the SeedViewer ==

'''[[SEED_Viewer_Manual|Home Page]]'''

'''[[SEED_Viewer_Manual/Menu|Menu]]'''

'''[[SEED_Viewer_Manual/Annotation|Annotation]]'''

'''[[SEED_Viewer_Manual/AlignSeqs|Alignment Page]]'''

'''[[SEED_Viewer_Manual/BLASTOrganism|BLAST against an organism]]'''

'''[[SEED_Viewer_Manual/BLASTDotPlot|BLAST Dot Plot]]'''

'''[[SEED_Viewer_Manual/DownloadOrganism|Download Organism]]'''

'''[[SEED_Viewer_Manual/GenomeBrowser|Browse Genome]]'''

'''[[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]]'''

'''[[SEED_Viewer_Manual/ContigView|Contig View]]'''

'''[[SEED_Viewer_Manual/Evidence|Evidence]]'''

'''[[SEED_Viewer_Manual/FIGfams|FIGfams]]'''

'''[[SEED_Viewer_Manual/FIGfamsRelease|FIGfam Release]]'''

'''[[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer]]'''

'''[[SEED_Viewer_Manual/FunctionalRoles|Functional Role]]'''

'''[[SEED_Viewer_Manual/HomologClusters|Homolog Clusters]]'''

'''[[SEED_Viewer_Manual/KEGG|KEGG Page]]'''

'''[[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]]'''

'''[[SEED_Viewer_Manual/OrganismPage|Organism Page]]'''

'''[[SEED_Viewer_Manual/OrganismSelect|Organism Select]]'''

'''[[SEED_Viewer_Manual/SearchGene|Search Gene]]'''

'''[[SEED_Viewer_Manual/Scenarios|Scenarios]]'''

'''[[SEED_Viewer_Manual/ShowSeqs|Sequence]]'''

'''[[SEED_Viewer_Manual/Subsystems|Subsystems Page]]'''

SEED Viewer Manual/Subsystems

2008-12-12T14:13:22Z

DanielaBartels: /* Scenarios */

== Subsystems ==

A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system.

The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. The last tab displays the [[Glossary#Scenarios|Scenarios]] for the subsystem.

=== Diagram ===

The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram.

The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green.

[[Image:SubsystemDiagram.png]]

=== Functional Roles ===

This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function.

The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet.

The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role.

The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED.

GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool.

The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column.

[[Image:SubsystemFRs.png]]

=== Spreadsheet ===

The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem.

The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name.

The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column.

For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[Glossary#Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''.

The Variant Code '''-1''' means that the organism has no active variant of this subsystem, it is not implement this organism.

'''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes.

The next column is used to filter active or inactive variants. If you want to see only the active ones (default), enter '''yes''' into the filter in the column header. For seeing only the not active ones, enter '''no'''. No input in this field will show all variants.

All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table). Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism.

The control table above the spreadsheet table lets you change the display in the table:

Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column.

The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display.

[[Image:SubsystemSpreadsheet.png]]

=== Description ===

The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest.

=== Additional Notes ===

As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user.

=== Scenarios ===

The table shows all scenarios that occur in the subsystem. You can see the scenario name, the '''Input Compounds''', the '''Output Compounds''' and a checkbox to decide if you want to see the scenario painted on the [http://www.genome.jp/kegg/ KEGG] map below. If you change the selection of scenarios to paint on the map, click the button '''Paint Map(s)''' to reload the map.

You can also select an organism to highlight on the map. Therefore, click the '''Select Organism''' button to get an [[SEED_Viewer_Manual/OrganismSelect|Organism Select]]. After choosing an organism, click the button '''Highlight Reactions for Organism''' to mark the enzymes present in the organism with black boxes.

[[Image:SubsystemScenTabs.png]]

The [http://www.genome.jp/kegg/ KEGG] map is the first tab of a [[WebComponents/Tabview|TabView]]. The header of the tab includes a link to the map at [http://www.genome.jp/kegg/ KEGG]. Each enzyme in the map is painted with all colors of the scenarios it is part of. A color legend is presented on the right side of the map.

The second tab of the [[WebComponents/Tabview|TabView]] shows all reactions that are not shown on the map, but are part of the subsystem.

[[Image:SubsystemScenarios.png]]

SEED Viewer Manual/IMGMAPTEST

2008-12-12T10:23:33Z

DanielaBartels:

SEED Viewer Manual/IMGMAPTEST

2008-12-12T10:22:28Z

DanielaBartels:

SEED Viewer Manual/IMGMAPTEST

2008-12-12T10:20:41Z

DanielaBartels:

WebComponents/ListSelect

2008-12-08T13:49:12Z

DanielaBartels: /* List Select */

== List Select ==

This Component is used to select a number of items from a list. Usually, it is bound to a table where it adds additional columns from the list.

To select an item to add, mark the item and then the right arrow to put it into the right list. To remove it, mark it in the right list and click the left button to put it back.

The table the list select is bound to should update automatically.

[[Image:ListSelect.png]]

File:ListSelect.png

2008-12-08T13:40:09Z

DanielaBartels:

WebComponents/ListSelect

2008-12-08T13:39:47Z

DanielaBartels: /* List Select */

== List Select ==

[[Image:ListSelect.png]]

WebComponents/ListSelect

2008-12-08T13:39:35Z

DanielaBartels:

== List Select ==

[Image:ListSelect.png]

SEED Viewer Manual/Evidence

2008-12-08T13:31:22Z

DanielaBartels: /* Similarities */

The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''.

If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]].

== Visual Protein Evidence ==

After loading the Evidence Page, the first tab of the [[WebComponents/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features.

=== Location ===

'''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein.

[[Image:EvidenceLocation.png]]

=== Domains ===

This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein).

Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar.

[[Image:EvidenceDomain.png]]

=== Similarities ===

This section graphically lists evidence for similarities to other features in the SEED and other databases. The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color.

Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. To the right of the checkbox you can find the [[Glossary#Functional role|functional role]] of the hit feature.

The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area.

If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two functions via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format.

[[Image:EvidenceSims1.png]]

[[Image:EvidenceHoverSim.png]]

To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view.

[[Image:EvidenceFil1.png]]

== Tabular Protein Evidence ==

Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab.

=== Similarities ===

The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED and other databases, as described at [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit.

The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]].

The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''.

The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence''').

The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color.

'''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell.

There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]].

The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table.

[[Image:EvidenceSims2.png]]

You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a [[WebComponents/ListSelect|List Select]] with a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table.

[[Image:EvidenceFilter.png]]

=== Domains ===

This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein).

The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain.

The table can be exported using the '''export table''' button.

Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar.

[[Image:EvidenceDomTable.png]]

=== Identical Proteins ===

'''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity.

The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias.

[[Image:EvidenceEIPs.png]]

=== Functionally Coupled ===

This [[WebComponents/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature.

[[Image:EvidenceFCs.png]]

SEED Viewer Manual/Evidence

2008-12-08T13:30:31Z

DanielaBartels: /* Similarities */

The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''.

If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]].

== Visual Protein Evidence ==

After loading the Evidence Page, the first tab of the [[WebComponents/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features.

=== Location ===

'''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein.

[[Image:EvidenceLocation.png]]

=== Domains ===

This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein).

Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar.

[[Image:EvidenceDomain.png]]

=== Similarities ===

This section graphically lists evidence for similarities to other features in the SEED and other databases. The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color.

Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. To the right of the checkbox you can find the [[Glossary#Functional role|functional role]] of the hit feature.

The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area.

If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two functions via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format.

[[Image:EvidenceSims1.png]]

[[Image:EvidenceHoverSim.png]]

To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view.

[[Image:EvidenceFil1.png]]

== Tabular Protein Evidence ==

Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab.

=== Similarities ===

The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED and other databases, as described at [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit.

The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]].

The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''.

The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence''').

The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color.

'''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell.

There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]].

The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table.

[[Image:EvidenceSims2.png]]

You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a [[WebComponents/ListSelect]] with a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table.

[[Image:EvidenceFilter.png]]

=== Domains ===

This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein).

The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain.

The table can be exported using the '''export table''' button.

Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar.

[[Image:EvidenceDomTable.png]]

=== Identical Proteins ===

'''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity.

The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias.

[[Image:EvidenceEIPs.png]]

=== Functionally Coupled ===

This [[WebComponents/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature.

[[Image:EvidenceFCs.png]]

SEED Viewer Manual/Editing Capabilities/ChromosomalClusters

2008-12-08T13:26:23Z

DanielaBartels: /* Details table */

== Editing Capabilities - Chromosomal Clusters ==

This page can be accessed from a [[SEED_Viewer_Manual/Annotation#Chromosomal Clusters|Chromosomal Clusters]] view, using the button '''annotate clusters''' (only visible if you have editing rights for the genome).

=== Overview Table ===

The first table on the page lists all sets of protein visible in the Chromosomal Clusters view. The set numbers in the first column are the set numbers from the view. The second column ('''#features''') shows the number of features in the set. '''#functions''' depicts how many different functions the features in the set have. One of the functions is displayed in the column '''first function'''. Whenever there is more than one function, the cell in the next column will be painted in red, as it is not '''consistent''', else green. With the check boxes in the last column, you can turn on and off the details tables for each of the sets.

Above the table, there are four buttons to turn on/off the details tables. '''show all''' will remove previous filtering and show you all details tables again. '''show none''' will remove all details tables, so that you can afterwards select single ones you'd like to see. '''show consistenct''' and '''show inconsistent''' is related to the '''consistent''' column in the table. It will display the details tables with a consistent or an inconsistent set, respectively.

[[Image:Chromosomal1.png]]

=== Details table ===

As a default, for each set you will get a details table in the following. These list all the features in the set. The set number is displayed in the first column. '''Organism''' is the genome the feature stems from. If there are more than one occurrence of features in the set for one genome, they are numbered in the '''Occ''' column. If there is a [http://www.uniprot.org UniProt] alias for the feature, the ID and the function of this alias will be shown in the next two columns.

The IDs of the features in the next column '''Feature''' link to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. If the feature is in a subsystem, you will find one or many (comma-separated) numbers in the '''SS''' column. Hovering over the cell will display a tooltip with the names of the subsystems. The column '''Ev''' shows Evidence Codes for the feature. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]].

The length of the feature is shown in the next column ('''Ln'''). Its current function can be found in the column '''Function'''. Same colors in this column indicate same functions. Links to a [[SEED_Viewer_Manual/FIGfamViewer|FIGfam]] a feature is member of are displayed in the last column.

Editing the function for the features in the Details table is done by checking a function or entering a new one, then clicking the '''annotate''' button. You can select a UniProt function, or one of the other feature's functions. If you want to use a new one, enter it in the '''new function''' text field and check the radio box next to it. The new function will be used to annotate all features that are checked in the '''Feature''' column. You will only be able to check features you can edit. In this example, only the ''Escherichia coli K12'' can be edited, so you will find a checkbox only for this feature.

To align features in the [[SEED_Viewer_Manual/AlignSeqs|Alignment Page]], check the features of interest and press the button '''align'''.

The buttons '''check all''', '''uncheck all''' and '''check to last checked''' can be used for the check boxes of the features, which is especially important for large tables.

[[Image:Chromosomal2.png]]

SEED Viewer Manual/Editing Capabilities/ChromosomalClusters

2008-12-08T12:01:15Z

DanielaBartels: /* Details table */

SEED Viewer Manual/Editing Capabilities/ChromosomalClusters

2008-12-08T11:56:01Z

DanielaBartels: /* Details table */

SEED Viewer Manual/Evidence

2008-12-08T11:51:33Z

DanielaBartels: /* Visual Protein Evidence */

The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''.

If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]].

== Visual Protein Evidence ==

After loading the Evidence Page, the first tab of the [[WebComponents/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features.

=== Location ===

'''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein.

[[Image:EvidenceLocation.png]]

=== Domains ===

This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein).

Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar.

[[Image:EvidenceDomain.png]]

=== Similarities ===

This section graphically lists evidence for similarities to other features in the SEED and other databases. The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color.

Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. To the right of the checkbox you can find the [[Glossary#Functional role|functional role]] of the hit feature.

The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area.

If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two functions via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format.

[[Image:EvidenceSims1.png]]

[[Image:EvidenceHoverSim.png]]

To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view.

[[Image:EvidenceFil1.png]]

== Tabular Protein Evidence ==

Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab.

=== Similarities ===

The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED and other databases, as described at [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit.

The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]].

The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''.

The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence''').

The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color.

'''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell.

There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]].

The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table.

[[Image:EvidenceSims2.png]]

You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table.

[[Image:EvidenceFilter.png]]

=== Domains ===

This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein).

The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain.

The table can be exported using the '''export table''' button.

Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar.

[[Image:EvidenceDomTable.png]]

=== Identical Proteins ===

'''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity.

The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias.

[[Image:EvidenceEIPs.png]]

=== Functionally Coupled ===

This [[WebComponents/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature.

[[Image:EvidenceFCs.png]]

File:Chromosomal2.png

2008-12-08T11:12:08Z

DanielaBartels:

SEED Viewer Manual/Editing Capabilities/ChromosomalClusters

2008-12-08T11:11:45Z

DanielaBartels: /* Overview Table */

SEED Viewer Manual/Editing Capabilities/ChromosomalClusters

2008-12-08T10:56:07Z

DanielaBartels: /* Editing Capabilities - Chromosomal Clusters */

SEED Viewer Manual/Editing Capabilities/ChromosomalClusters

2008-12-08T10:48:48Z

DanielaBartels: /* Editing Capabilities - Chromosomal Clusters */

File:Chromosomal1.png

2008-12-08T10:43:53Z

DanielaBartels:

SEED Viewer Manual/Editing Capabilities/ChromosomalClusters

2008-12-08T10:43:32Z

DanielaBartels: /* Editing Capabilities - Chromosomal Clusters */

SEED Viewer Manual/Editing Capabilities/ChromosomalClusters

2008-12-05T17:01:56Z

DanielaBartels:

SEED Viewer Manual/Editing Capabilities/CreateFeature

2008-12-05T16:02:34Z

DanielaBartels: /* Actions panel */

== Editing Capabilities - Create Feature ==

This page lets you create a new protein feature. It consists of three parts, a Control [[WebComponents/Tabview|TabView]], an '''Actions''' panel and the '''Sequence Table'''.

=== Control TabView ===

In the first tab of this TabView, you can put in a function for your newly created feature by just entering it into the text field.
Below that, you can see two text fields for controlling ''Up/Downstream Nucleotides'''. As you usually enter this page from the [[SEED_Viewer_Manual/SearchGene|Search Gene Page]], you have a hit region defined in which the feature is to be located. The numbers you can enter are the number of upstream and downstream nucleotides of the hit you want to see in the '''Sequence Table'''. After entering your numbers, click the '''update''' button in the '''Actions''' panel

The second tab of the TabView lists all codons of the genetic code. Here, you can select the start codons that are possible for the genome you want to create a feature in. Pre-selected are the standard start codons that are usually used for bacterial genomes. You can choose a different set of codons and press the button '''update''' in the '''Actions''' panel to change the view in the '''Sequence Table'''.

The genetic code can have small differences from the default genetic code in some organisms. You can change the standard genetic code in the third tab of the TabView. For each triplet, you can see the default amino acid that is usually used in organisms. If you want to change this for a triplet, click the respective drop down box and choose the right amino acid. To make the changes visible in the '''Sequence Table''', press the '''update''' button in the '''Actions''' panel again.

[[Image:CNFTab.png]]

=== Actions panel ===

The actions panel consists of three buttons. The '''update''' will let you update the '''Sequence Table''' with new parameters you can type in the '''Control TabView'''.

Clicking the second button, '''blastp''' will perform a protein based BLAST of the region selected in the '''Sequence Table'''. For this, you have to choose a '''start'''codon in the table. The sequence taken for the BLAST comparison is the translated protein sequence of the region from that start codon to the next stop codon in that frame. Note that you do not select a '''stop''' codon. If you select a '''stop''' codon, this will be ignored for defining the sequence region.

The blast search will result in a [[WebComponents/Table|table]] with all hit proteins. The table shows the hit feature and it's function. You can select a function in this table for the new protein you want to create, instead of putting in a new on in the '''Control TabView''' above.

If you have selected a '''start''' codon in the '''Sequence Table''', you can also directly create the feature for that region if you are sure about it. Clicking the '''create''' button will do that.

[[Image:CNFActions.png]]

=== Sequence Table ===

The sequence table is a table of the codons in a genomic region. Each cell represents a triplet. The first line of each line is the translation of that triplet to amino acid. A ''*'' stands for a '''stop''' codon. The second line shows the actual triplet (the codon).

The third line can have dots (...), forward arrows (>>>) or reverse arrows (<<<). Dots mean that there not feature overlaps this part of the region. Forward arrows represent a feature on the forward strand, reverse arrows on the reverse strand. This way, you can see if the feature you want to create overlaps with an already present feature in that region.

The fourth line sometimes has a check box or a radio box. Radio boxes are shown for every '''start''' codon. A cell with a start codon is also painted in a green color. Check a radio box to mark the start of the feature. RBS binding sites (purple colored cells) can help to determine the right start codon. Check boxes are used for '''stop''' codons (cells with red color). Check the check box of a '''stop''' codon to ignore it, meaning that the feature be continue to the next (unchecked) '''stop''' codon.

[[Image:CreateNewFeature.png]]

SEED Viewer Manual/Editing Capabilities/CreateFeature

2008-12-05T15:19:25Z

DanielaBartels: /* Sequence Table */

== Editing Capabilities - Create Feature ==

This page lets you create a new protein feature. It consists of three parts, a Control [[WebComponents/Tabview|TabView]], an '''Actions''' panel and the '''Sequence Table'''.

=== Control TabView ===

In the first tab of this TabView, you can put in a function for your newly created feature by just entering it into the text field.
Below that, you can see two text fields for controlling ''Up/Downstream Nucleotides'''. As you usually enter this page from the [[SEED_Viewer_Manual/SearchGene|Search Gene Page]], you have a hit region defined in which the feature is to be located. The numbers you can enter are the number of upstream and downstream nucleotides of the hit you want to see in the '''Sequence Table'''. After entering your numbers, click the '''update''' button in the '''Actions''' panel

The second tab of the TabView lists all codons of the genetic code. Here, you can select the start codons that are possible for the genome you want to create a feature in. Pre-selected are the standard start codons that are usually used for bacterial genomes. You can choose a different set of codons and press the button '''update''' in the '''Actions''' panel to change the view in the '''Sequence Table'''.

The genetic code can have small differences from the default genetic code in some organisms. You can change the standard genetic code in the third tab of the TabView. For each triplet, you can see the default amino acid that is usually used in organisms. If you want to change this for a triplet, click the respective drop down box and choose the right amino acid. To make the changes visible in the '''Sequence Table''', press the '''update''' button in the '''Actions''' panel again.

[[Image:CNFTab.png]]

=== Actions panel ===

The actions panel consists of three buttons. The '''update''' will let you update the '''Sequence Table''' with new parameters you can type in the '''Control TabView'''.

Clicking the second button, '''blastp''' will perform a protein based BLAST of the region selected in the '''Sequence Table'''. For this, you have to choose a '''start'''codon in the table. The sequence taken for the BLAST comparison is the translated protein sequence of the region from that start codon to the next stop codon in that frame. Note that you do not select a '''stop''' codon. If you select a '''stop''' codon, this will be ignored for defining the sequence region.

If you have selected a '''start''' codon in the '''Sequence Table''', you can also directly create the feature for that region if you are sure about it. Clicking the '''create''' button will do that.

[[Image:CNFActions.png]]

=== Sequence Table ===

The sequence table is a table of the codons in a genomic region. Each cell represents a triplet. The first line of each line is the translation of that triplet to amino acid. A ''*'' stands for a '''stop''' codon. The second line shows the actual triplet (the codon).

The third line can have dots (...), forward arrows (>>>) or reverse arrows (<<<). Dots mean that there not feature overlaps this part of the region. Forward arrows represent a feature on the forward strand, reverse arrows on the reverse strand. This way, you can see if the feature you want to create overlaps with an already present feature in that region.

The fourth line sometimes has a check box or a radio box. Radio boxes are shown for every '''start''' codon. A cell with a start codon is also painted in a green color. Check a radio box to mark the start of the feature. RBS binding sites (purple colored cells) can help to determine the right start codon. Check boxes are used for '''stop''' codons (cells with red color). Check the check box of a '''stop''' codon to ignore it, meaning that the feature be continue to the next (unchecked) '''stop''' codon.

[[Image:CreateNewFeature.png]]

SEED Viewer Manual/Editing Capabilities/CreateFeature

2008-12-05T15:16:43Z

DanielaBartels: /* Actions panel */

== Editing Capabilities - Create Feature ==

This page lets you create a new protein feature. It consists of three parts, a Control [[WebComponents/Tabview|TabView]], an '''Actions''' panel and the '''Sequence Table'''.

=== Control TabView ===

In the first tab of this TabView, you can put in a function for your newly created feature by just entering it into the text field.
Below that, you can see two text fields for controlling ''Up/Downstream Nucleotides'''. As you usually enter this page from the [[SEED_Viewer_Manual/SearchGene|Search Gene Page]], you have a hit region defined in which the feature is to be located. The numbers you can enter are the number of upstream and downstream nucleotides of the hit you want to see in the '''Sequence Table'''. After entering your numbers, click the '''update''' button in the '''Actions''' panel

The second tab of the TabView lists all codons of the genetic code. Here, you can select the start codons that are possible for the genome you want to create a feature in. Pre-selected are the standard start codons that are usually used for bacterial genomes. You can choose a different set of codons and press the button '''update''' in the '''Actions''' panel to change the view in the '''Sequence Table'''.

The genetic code can have small differences from the default genetic code in some organisms. You can change the standard genetic code in the third tab of the TabView. For each triplet, you can see the default amino acid that is usually used in organisms. If you want to change this for a triplet, click the respective drop down box and choose the right amino acid. To make the changes visible in the '''Sequence Table''', press the '''update''' button in the '''Actions''' panel again.

[[Image:CNFTab.png]]

=== Actions panel ===

The actions panel consists of three buttons. The '''update''' will let you update the '''Sequence Table''' with new parameters you can type in the '''Control TabView'''.

Clicking the second button, '''blastp''' will perform a protein based BLAST of the region selected in the '''Sequence Table'''. For this, you have to choose a '''start'''codon in the table. The sequence taken for the BLAST comparison is the translated protein sequence of the region from that start codon to the next stop codon in that frame. Note that you do not select a '''stop''' codon. If you select a '''stop''' codon, this will be ignored for defining the sequence region.

If you have selected a '''start''' codon in the '''Sequence Table''', you can also directly create the feature for that region if you are sure about it. Clicking the '''create''' button will do that.

[[Image:CNFActions.png]]

=== Sequence Table ===

The sequence table is a table of the codons in a genomic region. Each cell represents a triplet. The first line of each line is the translation of that triplet to amino acid. A ''*'' stands for a '''stop''' codon. The second line shows the actual triplet (the codon).

The third line can have dots (...), forward arrows (>>>) or reverse arrows (<<<). Dots mean that there not feature overlaps this part of the region. Forward arrows represent a feature on the forward strand, reverse arrows on the reverse strand. This way, you can see if the feature you want to create overlaps with an already present feature in that region.

The fourth line sometimes has a check box or a radio box. Radio boxes are shown for every '''start''' codon. Check a radio box to mark the start of the feature. Check boxes are used for '''stop''' codons. Check the check box of a '''stop''' codon to ignore it, meaning that the feature be continue to the next (unchecked) '''stop''' codon.

[[Image:CreateNewFeature.png]]

SEED Viewer Manual/Editing Capabilities/CreateFeature

2008-12-05T15:06:20Z

DanielaBartels: /* Actions panel */

SEED Viewer Manual/Editing Capabilities/CreateFeature

2008-12-05T15:05:46Z

DanielaBartels: /* Actions panel */

SEED Viewer Manual/Editing Capabilities/CreateFeature

2008-12-05T13:46:03Z

DanielaBartels: /* Control TabView */

SEED Viewer Manual/Editing Capabilities/CreateFeature

2008-12-05T13:45:13Z

DanielaBartels: /* Editing Capabilities - Create Feature */

File:CreateNewFeature.png

2008-12-05T13:24:26Z

DanielaBartels:

File:CNFActions.png

2008-12-05T13:24:04Z

DanielaBartels:

File:CNFTab.png

2008-12-05T13:23:47Z

DanielaBartels:

SEED Viewer Manual/Editing Capabilities/CreateFeature

2008-12-05T13:23:03Z

DanielaBartels:

== Editing Capabilities - Create Feature ==

[[Image:CNFTab.png]]

[[Image:CNFActions.png]]

[[Image:CreateNewFeature.png]]

SEED Viewer Manual/Editing Capabilities

2008-12-05T11:34:59Z

DanielaBartels: /* Editing capabilities in the SeedViewer */

== Editing capabilities in the SeedViewer ==

[[SEED_Viewer_Manual/Editing_Capabilities/Annotation|Annotation Page]]

[[SEED_Viewer_Manual/Editing_Capabilities/ChromosomalClusters|Chromosomal Clusters Page]]

[[SEED_Viewer_Manual/Editing_Capabilities/Evidence|Evidence Page]]

[[SEED_Viewer_Manual/Editing_Capabilities/SearchGene|Search Gene Page]]

[[SEED_Viewer_Manual/Editing_Capabilities/CreateFeature|Create new Feature Page]]

[[SEED_Viewer_Manual/EditLiterature|Edit Literature for a feature]]

SEED Viewer Manual/Editing Capabilities/SearchGene

2008-12-05T11:33:11Z

DanielaBartels: /* Editing Capabilities - Search Gene Page */

== Editing Capabilities - Search Gene Page ==

If you have the right to edit the genome for which the [[SEED_Viewer_Manual/SearchGene|Search Gene Page]] is displayed, you will additional options to '''annotate a found feature''' or '''create a new feature'''.

=== Annotate a found feature ===

The BLAST [[WebComponents/Table|table]] now has an additional column on the left to check the hit feature. If you click the newly appeared button '''Assign Role''', you will annotate the hit feature with the function of the matched feature.

The arrows in the graphics in the '''Is the gene maybe not called?''' section are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] where you will also have the option to annotate the feature if you have the right to [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|edit the feature]].

=== Create new feature ===

If you have found a missing feature in the tblastn graphics, you can click the hit (marked by a ''Q'') to get to the [[SEED_Viewer_Manual/Editing_Capabilities/CreateFeature|Create Feature]] page.

SEED Viewer Manual/Editing Capabilities/SearchGene

2008-12-05T11:03:36Z

DanielaBartels:

SEED Viewer Manual/GenomeBrowser

2008-12-05T10:58:48Z

DanielaBartels: /* The Control TabView */

== Genome Browser ==

The Genome Browser enables you to view the features of a genome in their genomic context. The page is divided into three parts, a Control [[WebComponents/Tabview|TabView]], the Six Frame View, and a [[WebComponents/Table|table]] showing all features of an organism.

=== The Six Frame View ===

The six frame view represents the six reading frames for proteins (-3, -2, -1, 1, 2, 3). Blue arrows are printed representing protein features. Their direction depicts the strand of the protein (- or +).

As RNA features (tRNAs, rRNAs, or other genomic features like binding sites) have no reading frames. They can be found in the middle line of the image, represented by little blue boxes.

Hovering over a feature will show a tooltip containing information about the feature, including the name, the position in the genome, the [[Glossary#Functional_role|functional role]] and the [[Glossary#Subsystem|subsystem(s)]] it's in.

[[Image:GenomeBrowser6fw.png]]

=== The Control TabView ===

Controlling the Six Frame View can be done using the first tab ('''Location''') of the Control TabView. You can choose a location the of the genome you want to view by selecting a contig in the '''contig''' drop down menu and stating a '''start position''' on that contig. The zoom of the window can be changed using the '''window''' drop down box.

In addition, features can be colored by different metaphors: by subsystem, by filter options of the Feature Table (the features that are present in the table after filtering it will be colored) or by a user defined list you can specify in the '''Upload List''' tab.

Click the button '''Draw''' after making your selections. The arrows '''<=''' and '''=>''' will shift the window over the contig sequence.

If you have selected a feature in the Six Frame View, the second tab ('''Focus''') will show you information about the feature (the same information you can find in the tooltip by hovering over the feature). Additionally, you will get three buttons that lead to pages that show more detailed information about the selected feature.

The button '''zoom to sequence''' will show you the '''[[SEED_Viewer_Manual/ContigView|DNA to Protein]]''' page depicting a detailed sequence view including the DNA sequence, a six frame view of the translation to protein and other features of the sequence in the area of the selected feature.

Clicking '''details page''' leads to the [[SEED_Viewer_Manual/Annotation|Annotation]] page of the feature. You will see all known details about the feature, as well as the [[SEED_Viewer_Manual/Annotation#CompareRegions|Compare regions view]] centered on the feature.

The '''evidence''' button leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of Similarities and protein domains.

'''Upload a list''' - will let you upload a list of locations of BLAST hits of the form (Contig, Start, Stop, ID). The list has to be in plain text format, meaning not an Excel table. If you have an Excel table containing the information, save the list as '''text (tab delimited)''' in Excel. If you have successfully uploaded a list, you will now be able to navigate the regions in your list. They are shown on the middle line in the Six Frame View in form of little boxes.

[[Image:GenomeBrowserLoc.png]]

=== The Feature Table ===

The Feature Table shows all features present in your organism in a [[WebComponents/Table|table]]. Information you can see for a feature are its ID, Type (e.g. CDS, RNA and others), its locations (Contig, Start, Stop) and length as well as the functional role it's annotated with and the subsystems it belongs to. The button in the last column (Region) will center the Six Frame View on this feature and select it.

[[Image:GenomeBrowserFeat.png]]

SEED Viewer Manual/Subsystems

2008-12-05T10:52:16Z

DanielaBartels: /* Spreadsheet */

== Subsystems ==

A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system.

The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. The last tab displays the [[Glossary#Scenarios|Scenarios]] for the subsystem.

=== Diagram ===

The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram.

The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green.

[[Image:SubsystemDiagram.png]]

=== Functional Roles ===

This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function.

The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet.

The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role.

The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED.

GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool.

The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column.

[[Image:SubsystemFRs.png]]

=== Spreadsheet ===

The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem.

The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name.

The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column.

For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[Glossary#Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''.

The Variant Code '''-1''' means that the organism has no active variant of this subsystem, it is not implement this organism.

'''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes.

The next column is used to filter active or inactive variants. If you want to see only the active ones (default), enter '''yes''' into the filter in the column header. For seeing only the not active ones, enter '''no'''. No input in this field will show all variants.

All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table). Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism.

The control table above the spreadsheet table lets you change the display in the table:

Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column.

The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display.

[[Image:SubsystemSpreadsheet.png]]

=== Description ===

The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest.

=== Additional Notes ===

As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user.

=== Scenarios ===

The table shows all scenarios that occur in the subsystem. You can see the scenario name, the '''Input Compounds''', the '''Output Compounds''' and a checkbox to decide if you want to see the scenario painted on the [http://www.genome.jp/kegg/ KEGG] map below. If you change the selection of scenarios to paint on the map, click the button '''Paint Map(s)''' to reload the map.

You can also select an organism to highlight on the map. Therefore, click the '''Select Organism''' button to get an [[SEED_Viewer_Manual/OrganismSelect]]. After choosing an organism, click the button '''Highlight Reactions for Organism''' to mark the enzymes present in the organism with black boxes.

[[Image:SubsystemScenTabs.png]]

The [http://www.genome.jp/kegg/ KEGG] map is the first tab of a [[WebComponents/Tabview|TabView]]. The header of the tab includes a link to the map at [http://www.genome.jp/kegg/ KEGG]. Each enzyme in the map is painted with all colors of the scenarios it is part of. A color legend is presented on the right side of the map.

The second tab of the [[WebComponents/Tabview|TabView]] shows all reactions that are not shown on the map, but are part of the subsystem.

[[Image:SubsystemScenarios.png]]

SEED Viewer Manual/AlignSeqs

2008-12-05T10:49:32Z

DanielaBartels: /* Align Sequences */

== Align Sequences ==

This page is usually loaded if you have selected a number of features in e.g. the [[SEED_Viewer_Manual/Evidence|Evidence Page]] and pressed an '''Align Sequences''' button. Here, the alignment is presented. The alignment software that is used is [http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html T-Coffee], a method for fast and accurate multiple sequence alignment.

On the top of the alignment, you can see a color legend for aligned regions. Below, the multiple alignment for all chosen features is displayed.

[[Image:AlignSeqs.png]]

SEED Viewer Manual/AlignSeqs

2008-12-05T10:49:01Z

DanielaBartels: /* Align Sequences */

SEED Viewer Manual/AlignSeqs

2008-12-05T10:44:59Z

DanielaBartels: /* Align Sequences */

== Align Sequences ==

[http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html T-Coffee]

[[Image:AlignSeqs.png]]