SEED Viewer Manual/HomologClusters - Revision history

DanielaBartels: /* Homolog cluster */

2008-11-24T15:05:12Z

Homolog cluster

DanielaBartels: /* Homolog cluster */

2008-11-24T14:49:11Z

Homolog cluster

DanielaBartels: /* Homolog cluster */

2008-11-24T14:48:45Z

Homolog cluster

DanielaBartels: /* Homolog cluster */

2008-11-24T14:46:31Z

Homolog cluster

DanielaBartels: /* Homolog cluster */

2008-11-24T14:46:08Z

Homolog cluster

DanielaBartels: /* Homolog cluster */

2008-11-24T14:34:27Z

Homolog cluster

DanielaBartels at 14:24, 24 November 2008

2008-11-24T14:24:09Z

DanielaBartels at 14:20, 24 November 2008

2008-11-24T14:20:36Z

New page

Genes who's relative position is conserved in at least four other species are functionally coupled

@@ Line 5: / Line 5: @@
 On the top of the page a small table shows some information about the query feature. The '''Input Feature ID''' links to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for the feature. The '''Organism''' link leads to the respective [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The '''Cluster Size''' depicts how many features in that organism belong to the computed cluster. The '''Function''' of the query peg is depicted next, as well as '''Other functions in the cluster''', meaning the functions of the other features in that genome that are computed to belong to the cluster.
-The following table of all features in the computed homolog cluster shows you the same information for each feature, as well as '''Aliases''' for that features in other databases.
+The following table of all features in the computed homolog cluster shows you the same information for each feature, as well as '''Aliases''' for that features in other databases. The column '''Cluster Functions''' includes the functions of the stated feature, which is marked in red.
 [[Image:HomologClusters.png]]

@@ Line 5: / Line 5: @@
 On the top of the page a small table shows some information about the query feature. The '''Input Feature ID''' links to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for the feature. The '''Organism''' link leads to the respective [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The '''Cluster Size''' depicts how many features in that organism belong to the computed cluster. The '''Function''' of the query peg is depicted next, as well as '''Other functions in the cluster''', meaning the functions of the other features in that genome that are computed to belong to the cluster.
-The following table of all features in the computed homolog cluster shows you the same information for each feature, as well as Aliases for that features in other databases.
+The following table of all features in the computed homolog cluster shows you the same information for each feature, as well as '''Aliases''' for that features in other databases.
 [[Image:HomologClusters.png]]

@@ Line 5: / Line 5: @@
 On the top of the page a small table shows some information about the query feature. The '''Input Feature ID''' links to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for the feature. The '''Organism''' link leads to the respective [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The '''Cluster Size''' depicts how many features in that organism belong to the computed cluster. The '''Function''' of the query peg is depicted next, as well as '''Other functions in the cluster''', meaning the functions of the other features in that genome that are computed to belong to the cluster.
+The following table of all features in the computed homolog cluster shows you the same information for each feature, as well as Aliases for that features in other databases.
 [[Image:HomologClusters.png]]

@@ Line 1: / Line 1: @@
 == Homolog cluster ==
-This page shows the homolog cluster table for a given feature, where ''homology'' is inferred by similarity score. The ''cluster'' is computed using [[Glossary#Functional Coupling|Functional coupling]] as a basis. For a given organism, only features which are in clusters are considered, and only a single feature (the one with the best similarity score) is reported. The table consists of maximal 50 homolog features, and the evalue cutoff is e -10.
+This page shows the homolog cluster table for a given feature, where ''homology'' is inferred by similarity score. The ''cluster'' is computed using [[Glossary#Functional coupling|Functional coupling]] as a basis. For a given organism, only features which are in clusters are considered, and only a single feature (the one with the best similarity score) is reported. The table consists of maximal 50 homolog features, and the evalue cutoff is e -10.
 On the top of the page a small table shows some information about the query feature. The '''Input Feature ID''' links to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for the feature. The '''Organism''' link leads to the respective [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The '''Cluster Size''' depicts how many features in that organism belong to the computed cluster. The '''Function''' of the query peg is depicted next, as well as '''Other functions in the cluster''', meaning the functions of the other features in that genome that are computed to belong to the cluster.

@@ Line 1: / Line 1: @@
 == Homolog cluster ==
-# returns the homolog cluster table, where 'homology' is inferred by similarity score.
+This page shows the homolog cluster table for a given feature, where ''homology'' is inferred by similarity score. The ''cluster'' is computed using [[Glossary#Functional Coupling|Functional coupling]] as a basis. For a given organism, only features which are in clusters are considered, and only a single feature (the one with the best similarity score) is reported. The table consists of maximal 50 homolog features, and the evalue cutoff is e -10.
-evalue: 1.0e-10
+On the top of the page a small table shows some information about the query feature. The '''Input Feature ID''' links to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for the feature. The '''Organism''' link leads to the respective [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The '''Cluster Size''' depicts how many features in that organism belong to the computed cluster. The '''Function''' of the query peg is depicted next, as well as '''Other functions in the cluster''', meaning the functions of the other features in that genome that are computed to belong to the cluster.
 [[Image:HomologClusters.png]]

← Older revision		Revision as of 14:34, 24 November 2008
Line 10:		Line 10:

	Genes who's relative position is conserved in at least four other species are functionally coupled		Genes who's relative position is conserved in at least four other species are functionally coupled
		+
		+	[[Image:HomologClusters.png]]

← Older revision		Revision as of 14:24, 24 November 2008
Line 1:		Line 1:
		+	== Homolog cluster ==
		+
		+	# returns the homolog cluster table, where 'homology' is inferred by similarity score.
		+	# For a given organism, only pegs which are in clusters are considered, and only
		+	# a single peg (the one with the best sim score) is reported.
		+
		+	evalue: 1.0e-10
		+
		+	maximal 50 homolog features
		+
	Genes who's relative position is conserved in at least four other species are functionally coupled		Genes who's relative position is conserved in at least four other species are functionally coupled