SEED Viewer Manual/MultiGenomeCompare - Revision history

DanielaBartels: /* Result */

2008-12-02T09:21:31Z

Result

DanielaBartels: /* Result */

2008-12-01T17:13:41Z

Result

DanielaBartels: /* Result */

2008-12-01T17:07:50Z

Result

DanielaBartels: /* Result */

2008-12-01T17:02:38Z

Result

DanielaBartels: /* Result */

2008-12-01T17:02:00Z

Result

DanielaBartels: /* Result */

2008-12-01T17:00:52Z

Result

DanielaBartels: /* Result */

2008-12-01T16:23:06Z

Result

DanielaBartels: /* Result */

2008-12-01T16:21:37Z

Result

DanielaBartels: /* Result */

2008-12-01T16:15:52Z

Result

DanielaBartels: /* Result */

2008-12-01T14:50:33Z

Result

@@ Line 40: / Line 40: @@
 [[Image:MCGResultc.png]]
-The circular image right to the table is a whole genome view for the reference genome. Each circle represents a projection of a comparison genome to the reference genome. Keep in mind that the table as well as the graphic only shows features of the comparison genomes, that are hit by the reference genome. The order of the features is determined by the reference genome.
+The circular image right to the table is a whole genome view for the reference genome. Each circle represents a projection of a comparison genome to the reference genome, in the same order as in the table. Keep in mind that the table as well as the graphic only shows features of the comparison genomes, that are hit by the reference genome. The order of the features is determined by the reference genome.
 If you click on a line in the graphics, the table will update and show the area that was clicked in the graphic. The red circle in the graphic determines the area the table currently displays.

@@ Line 34: / Line 34: @@
 [[SEED_Viewer_Manual/Annotation|Annotation]] page for the feature.
-The best BLAST hit of the query feature in the comparison genome is shown in three columns in the table ('''Hit''', '''Contig''' and '''Gene'''). The color of the hit is determined by the percent identity of the query and the hit. No color means there is no hit. The '''Hit''' column contains a '-' (no hit), 'uni' or 'bi'. The '''bi''' stands for ''bidirectional best hit'', meaning that the reverse hit from the comparison genome to the reference genome is also the best hit (That's not always true if a genome contains many close paralogs for a feature). If it's not a bidirectional hit, it shows '''uni''' for uni-directional. Each feature ID is again linked to the feature's [[SEED_Viewer_Manual/Annotation|Annotation Page]].
+The best BLAST hit of the query feature in the comparison genome is shown in three columns in the table ('''Hit''', '''Contig''' and '''Gene'''). The color of the hit is determined by the percent identity of the query and the hit. No color means there is no hit. The '''Hit''' column contains a '-' (no hit), 'uni' or 'bi'. The '''bi''' stands for ''bidirectional best hit'', meaning that the reverse hit from the comparison genome to the reference genome is also the best hit (That's not always true if a genome contains many close paralogs for a feature). If it's not a bidirectional hit, it shows '''uni''' for uni-directional. Each feature ID is again linked to the feature's [[SEED_Viewer_Manual/Annotation|Annotation Page]]. Hovering over a cell in the table will show a tooltip with some information about the feature.
-The contents of the table can be exported in ''tab-separated format'' using the '''export''' button on top of the table. The filters below the buttons refer to the percent identity for the features of each genome. You can choose to filter the table for the percent identity above or below a certain value for each genome, and also in combination. Use the button '''Clear all filters''' to reset the table.
+The contents of the table can be exported in ''tab-separated format'' using the '''export''' button on top of the table. The filters below the buttons refer to the percent identity for the features of each genome. You can choose to filter the table for the percent identity above or below a certain value for each genome, and also in combination. Use the button '''clear all filters''' to reset the table.
 [[Image:MCGResultc.png]]
 [[Image:MCGResult2.png]]

@@ Line 27: / Line 27: @@
 [[Image:MCGResulta.png]]
-The colored table below shows the outcome of the bidirectional BLAST comparisons between each comparison genome and the reference genome, projected on the reference genome. The colors in the table depicts the '''Percent protein sequence identity''' of each gene to it's ortholog in the reference genome. The legend on top of the table describes the coloring.
+The colored [[WebComponents/Table|table]] below shows the outcome of the bidirectional BLAST comparisons between each comparison genome and the reference genome, projected on the reference genome. The colors in the table depicts the '''Percent protein sequence identity''' of each gene to it's ortholog in the reference genome. The legend on top of the table describes the coloring.
 [[Image:MCGResultb.png]]
@@ Line 34: / Line 34: @@
 [[SEED_Viewer_Manual/Annotation|Annotation]] page for the feature.
-The best BLAST hit of the query feature in the comparison genome is shown in three columns in the table ('''Hit''', '''Contig''' and '''Gene'''). The color of the hit is determined by the percent identity of the query and the hit. No color means there is no hit. The '''Hit''' column contains a '-' (no hit), 'uni' or 'bi'. The '''bi''' stands for ''bidirectional best hit'', meaning that the reverse hit from the comparison genome to the reference genome is also the best hit (That's not always true if a genome contains many close paralogs for a feature). If it's not a bidirectional hit, it shows '''uni''' for uni-directional.
+The best BLAST hit of the query feature in the comparison genome is shown in three columns in the table ('''Hit''', '''Contig''' and '''Gene'''). The color of the hit is determined by the percent identity of the query and the hit. No color means there is no hit. The '''Hit''' column contains a '-' (no hit), 'uni' or 'bi'. The '''bi''' stands for ''bidirectional best hit'', meaning that the reverse hit from the comparison genome to the reference genome is also the best hit (That's not always true if a genome contains many close paralogs for a feature). If it's not a bidirectional hit, it shows '''uni''' for uni-directional. Each feature ID is again linked to the feature's [[SEED_Viewer_Manual/Annotation|Annotation Page]].
 [[Image:MCGResultc.png]]
 [[Image:MCGResult2.png]]

← Older revision		Revision as of 17:02, 1 December 2008
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	The best BLAST hit of the query feature in the comparison genome is shown in three columns in the table ('''Hit''', '''Contig''' and '''Gene'''). The color of the hit is determined by the percent identity of the query and the hit. No color means there is no hit. The '''Hit''' column contains a '-' (no hit), 'uni' or 'bi'. The '''bi''' stands for ''bidirectional best hit'', meaning that the reverse hit from the comparison genome to the reference genome is also the best hit (That's not always true if a genome contains many close paralogs for a feature). If it's not a bidirectional hit, it shows '''uni''' for uni-directional.		The best BLAST hit of the query feature in the comparison genome is shown in three columns in the table ('''Hit''', '''Contig''' and '''Gene'''). The color of the hit is determined by the percent identity of the query and the hit. No color means there is no hit. The '''Hit''' column contains a '-' (no hit), 'uni' or 'bi'. The '''bi''' stands for ''bidirectional best hit'', meaning that the reverse hit from the comparison genome to the reference genome is also the best hit (That's not always true if a genome contains many close paralogs for a feature). If it's not a bidirectional hit, it shows '''uni''' for uni-directional.

		+	[[Image:MCGResultc.png]]

	[[Image:MCGResult2.png]]		[[Image:MCGResult2.png]]

@@ Line 34: / Line 34: @@
 [[SEED_Viewer_Manual/Annotation|Annotation]] page for the feature.
-The best BLAST hit of the query feature in the comparison genome is shown in three columns in the table ('''Hit''', '''Contig''' and '''Gene'''). The color of the hit is determined by the percent identity of the query and the hit. No color means there is no hit. The '''Hit''' column contains a '-' (no hit), 'uni' or 'bi'. The '''bi''' stand for ''bidirectional best hit'', meaning that the reverse hit from the comparison genome to the reference genome is also the best hit (That's not always true if a genome contains many close paralogs for a feature). If it's not a bidirectional hit, it shows '''uni''' for uni-directional.
+The best BLAST hit of the query feature in the comparison genome is shown in three columns in the table ('''Hit''', '''Contig''' and '''Gene'''). The color of the hit is determined by the percent identity of the query and the hit. No color means there is no hit. The '''Hit''' column contains a '-' (no hit), 'uni' or 'bi'. The '''bi''' stands for ''bidirectional best hit'', meaning that the reverse hit from the comparison genome to the reference genome is also the best hit (That's not always true if a genome contains many close paralogs for a feature). If it's not a bidirectional hit, it shows '''uni''' for uni-directional.
 [[Image:MCGResult2.png]]

← Older revision		Revision as of 16:23, 1 December 2008
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	[[Image:MCGResulta.png]]		[[Image:MCGResulta.png]]

		+	The colored table below shows the outcome of the bidirectional BLAST comparisons between each comparison genome and the reference genome, projected on the reference genome. The colors in the table depicts the '''Percent protein sequence identity''' of each gene to it's ortholog in the reference genome. The legend on top of the table describes the coloring.

		+	[[Image:MCGResultb.png]]

−	The colored table below shows the outcome of the bidirectional BLAST comparisons between each comparison genome and the reference genome, projected on the reference genome. The colors in the table describe the '''Percent protein sequence identity''' of each gene to it's ortholog in the reference genome. The legend on top of the table

−	~~[[Image:MCGResultb.png]]~~

	[[Image:MCGResultc.png]]		[[Image:MCGResultc.png]]

← Older revision		Revision as of 14:50, 1 December 2008
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	[[Image:MCGResulta.png]]		[[Image:MCGResulta.png]]
		+
		+	The colored table below shows

	[[Image:MCGResultb.png]]		[[Image:MCGResultb.png]]