MG-RAST Numbers - Revision history

DanielPaarmann at 16:13, 3 October 2007

2007-10-03T16:13:55Z

DanielPaarmann: /* SeedViewer - Overview */

2007-10-03T16:03:28Z

SeedViewer - Overview

DanielPaarmann at 16:02, 3 October 2007

2007-10-03T16:02:30Z

DanielPaarmann: /* SeedViewer */

2007-10-03T15:55:53Z

SeedViewer

DanielPaarmann at 15:54, 3 October 2007

2007-10-03T15:54:18Z

DanielPaarmann at 15:17, 3 October 2007

2007-10-03T15:17:23Z

DanielPaarmann at 15:17, 3 October 2007

2007-10-03T15:17:04Z

Marland at 21:36, 2 October 2007

2007-10-02T21:36:16Z

DanielPaarmann at 17:53, 2 October 2007

2007-10-02T17:53:36Z

DanielPaarmann at 16:59, 2 October 2007

2007-10-02T16:59:08Z

@@ Line 1: / Line 1: @@
 The MG-RAST-Server and SEED Viewer offer you a large number of statistics and detailed numbers about your metagenome. The purpose of this page is to explain how we calculate these numbers and what they mean.
 === MG-RAST ===
@@ Line 61: / Line 62: @@
 : The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role.
 : '''Note:''' Not every coding sequence is part of a subsystem and a single coding sequence may fulfill functional roles in more than one subsystem (and thus be counted multiple times).
 === SeedViewer - Taxonomy ===

@@ Line 55: / Line 55: @@
 : * ''hypothetical''
 : This is the number of coding sequences which were assigned to be hypothetical (or a synonym)
 : '''Known bug:''' In some cases coding sequences do not have any functional assignment, but are not counted as hypothetical protein. That causes hypothetical and non-hypothetical not to add up to the total number of fragments.
 * ''Subsystem Counts''

@@ Line 50: / Line 50: @@
 * ''Protein Encoding Genes''
-: The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) and their sum should be the equal to the number of coding sequences displayed on the left.
+: The numbers are given in absolute and percent value. They should add up to 100% (given rounding error)
-: '''non-hypothetical'''
+: * ''non-hypothetical''
 : This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein''
-: '''hypothetical'''
+: * ''hypothetical''
 : This is the number of coding sequences which were assigned to be hypothetical (or a synonym)
 * ''Subsystem Counts''

@@ Line 27: / Line 27: @@
-=== SeedViewer ===
+=== SeedViewer - Overview ===
 On the ''Metagenome Overview'' page, there are a number of statistical counts about the selected metagenome:
@@ Line 57: / Line 57: @@
 * ''Subsystem Counts''
-: The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. Note that not every coding sequence is part of a subsystem and that a single CDS may be part of more than one subsytem.
+: The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role.
 === SeedViewer - Taxonomy ===

@@ Line 57: / Line 57: @@
 * ''Subsystem Counts''
-The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. Note that not every coding sequence is part of a subsystem and that a single CDS may be part of more than one subsytem.
+: The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. Note that not every coding sequence is part of a subsystem and that a single CDS may be part of more than one subsytem.
 === SeedViewer - Taxonomy ===

@@ Line 14: / Line 14: @@
 : This is the ''Total sequence length'' divided by the ''Number of sequences''
-* ''Longest sequence id'
+* ''Longest sequence id''
 : This is the identifier string of the longest sequence submitted.

@@ Line 1: / Line 1: @@
-The MG-RAST-Server and SEED Viewer offer you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean.
+The MG-RAST-Server and SEED Viewer offer you a large number of statistics and detailed numbers about your metagenome. The purpose of this page is to explain how we calculate these numbers and what they mean.
 === MG-RAST ===
-On the details page of your organism, you will find the following numbers:
+On the details page of your MG-Rast job, you will find the following numbers:
 * ''Number of sequences''
-: This is the total number of sequences submitted by the user for this genome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database.
+: This is the total number of sequences submitted by the user for this metagenome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database.
 * ''Total sequence length''
@@ Line 12: / Line 12: @@
 * ''Average read length''
-: This is the '''Total sequence length''' divided by the '''Number of sequences'''
+: This is the ''Total sequence length'' divided by the ''Number of sequences''
 * ''Longest sequence id'
@@ Line 32: / Line 32: @@
 * ''Size''
-: This is the number of basepairs (total length) of all of the sequences submiited for a given metagenome.
+: This is the number of basepairs (total length) of all of the sequences submitted for a given metagenome.
 : '''Known bug:''' Unfortunately there is currently a bug which shows a higher than actual sequence length. The MG-RAST Job Details page shows the correct sequence size.
@@ Line 44: / Line 44: @@
 * ''Number of Coding Sequences''
 : The number of protein encoding genes found in the submitted fragments that matched against our database.
-: '''Note:''' This number may be higher than the ''Number of Fragments'' if ...
+: '''Note:''' This number may be higher than the ''Number of Fragments'' if there are multiple matches on a single fragment.
 * ''Number of RNAs''
@@ Line 61: / Line 61: @@
 === SeedViewer - Taxonomy ===
-The taxnomic classification is calculated in several independent ways. First, all sequences are compared to the different rDNA databases: (1) RDP, (2)the European Ribosomal Database project, and (3)Greengenes. The criteria for a sequence being similar is a BLASTN E value < 1x10-5 and at least 50nt in the alignment.
+The taxonomic classification is calculated in several independent ways. First, all sequences are compared to the different rDNA databases: (1) RDP, (2)the European Ribosomal Database project, and (3)Greengenes. The criteria for a sequence being similar is a BLASTN E value < 1x10-5 and at least 50nt in the alignment.
 We also calculate the taxonomic profile of your sample from all the protein similarities computed to annotate the metagenome. The advantage of this approach is that we use a lot more data than is available for the 16S analysis, however, the disadvantage of this approach is that it is obviously limited to those genomes that are in our underlying SEED database.

@@ Line 9: / Line 9: @@
 * ''Total sequence length''
-: This is the sum of the lengths of all submitted sequences.
+: This is the sum of the lengths (bp) of all submitted sequences.
 * ''Average read length''
@@ Line 18: / Line 18: @@
 * ''Longest sequence length''
-: This is the length of the longest sequence submitted.
+: This is the length (bp) of the longest sequence submitted.
 * ''Shortest sequence id''
@@ Line 32: / Line 32: @@
 * ''Size''
-: This is the number of basepairs of sequence of this genome.
+: This is the number of basepairs (total length) of all of the sequences submiited for a given metagenome.
 : '''Known bug:''' Unfortunately there is currently a bug which shows a higher than actual sequence length. The MG-RAST Job Details page shows the correct sequence size.
 * ''Number of Fragments''
-: This is the number of fragments which included at least one coding sequence that could be matched to our database.
+: This is the number of submitted sequences which included at least one coding sequence that could be matched to our database.
 * ''Number of Subsystems''
-: The number of different subsystem in which at least one member was found in the fragments of the genome.
+: The number of different subsystems where one or more functional roles were found in the submitted fragments of the metagenome.
 * ''Number of Coding Sequences''
@@ Line 57: / Line 58: @@
 * ''Subsystem Counts''
 The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. Note that not every coding sequence is part of a subsystem and that a single CDS may be part of more than one subsytem.