SEED Viewer Manual/Editing Capabilities/CreateFeature - Revision history

DanielaBartels: /* Actions panel */

2008-12-05T16:02:34Z

Actions panel

DanielaBartels: /* Sequence Table */

2008-12-05T15:19:25Z

Sequence Table

DanielaBartels: /* Actions panel */

2008-12-05T15:16:43Z

Actions panel

DanielaBartels: /* Actions panel */

2008-12-05T15:06:20Z

Actions panel

DanielaBartels: /* Actions panel */

2008-12-05T15:05:46Z

Actions panel

DanielaBartels: /* Control TabView */

2008-12-05T13:46:03Z

Control TabView

DanielaBartels: /* Editing Capabilities - Create Feature */

2008-12-05T13:45:13Z

Editing Capabilities - Create Feature

DanielaBartels at 13:23, 5 December 2008

2008-12-05T13:23:03Z

New page

== Editing Capabilities - Create Feature ==

[[Image:CNFTab.png]]

[[Image:CNFActions.png]]

[[Image:CreateNewFeature.png]]

← Older revision		Revision as of 16:02, 5 December 2008
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	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.		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.		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.

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 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.
+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]]

← Older revision		Revision as of 15:16, 5 December 2008
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	[[Image:CNFActions.png]]		[[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]]		[[Image:CreateNewFeature.png]]

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 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.
+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.

@@ Line 6: / Line 6: @@
 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'''.
+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'''.

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 === Actions panel ===
 [[Image:CNFActions.png]]
 [[Image:CreateNewFeature.png]]

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 ==  Editing Capabilities - Create Feature ==
 [[Image:CNFTab.png]]
 [[Image:CNFActions.png]]
 [[Image:CreateNewFeature.png]]