Wikiomics:Orthologues - Revision history

Kristian Ullrich: /* References */

Kristian Ullrich — Wed, 08 Feb 2012 17:57:42 GMT

References

←Older revision		Revision as of 17:57, 8 February 2012
Line 28:		Line 28:
	# “Large-scale assignment of orthology: back to phylogenetics?.” Text, 2008. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760865/?tool=pubmed.		# “Large-scale assignment of orthology: back to phylogenetics?.” Text, 2008. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760865/?tool=pubmed.
	# “PLoS ONE: Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes.” http://www.plosone.org/article/fetchArticle.action?articleURI=info:doi/10.1371/journal.pone.0000383.		# “PLoS ONE: Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes.” http://www.plosone.org/article/fetchArticle.action?articleURI=info:doi/10.1371/journal.pone.0000383.
-		+	# "MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity." http://www.ncbi.nlm.nih.gov/pubmed/22217600

Kristian Ullrich: /* Other */

Kristian Ullrich — Wed, 08 Feb 2012 17:53:58 GMT

Other

←Older revision		Revision as of 17:53, 8 February 2012
Line 22:		Line 22:

	* [http://www.metazome.net/index.php Metazome] organizes the proteomes of twenty-four metazoans into gene families defined at nine ancestral nodes on the metazoan evolutionary tree. Shows synthenty.		* [http://www.metazome.net/index.php Metazome] organizes the proteomes of twenty-four metazoans into gene families defined at nine ancestral nodes on the metazoan evolutionary tree. Shows synthenty.
		+	* [http://chibba.pgml.uga.edu/mcscan2/ MCScanX] is an algorithm to scan multiple genomes or subgenomes to identify putative homologous chromosomal regions, then align these regions using genes as anchors.

	=References=		=References=

Darek Kedra: /* Orthologues retrival */

Darek Kedra — Mon, 07 Dec 2009 12:34:23 GMT

Orthologues retrival

←Older revision		Revision as of 12:34, 7 December 2009
Line 18:		Line 18:
	==Orthologues retrival==		==Orthologues retrival==
	* [http://orthomcl.cbil.upenn.edu/cgi-bin/OrthoMclWeb.cgi?rm=index OrthoMCL]		* [http://orthomcl.cbil.upenn.edu/cgi-bin/OrthoMclWeb.cgi?rm=index OrthoMCL]
		+
		+	=Other=
		+
		+	* [http://www.metazome.net/index.php Metazome] organizes the proteomes of twenty-four metazoans into gene families defined at nine ancestral nodes on the metazoan evolutionary tree. Shows synthenty.

	=References=		=References=

Darek Kedra: /* References */

Darek Kedra — Mon, 07 Dec 2009 11:13:11 GMT

References

←Older revision		Revision as of 11:13, 7 December 2009
Line 20:		Line 20:

	=References=		=References=
-	1. “Joining forces in the quest for orthologs,” Text, 2009, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768974/.	+	# “Joining forces in the quest for orthologs.” Text, 2009. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768974/.
-		+	# “Large-scale assignment of orthology: back to phylogenetics?.” Text, 2008. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760865/?tool=pubmed.
-	2. “Large-scale assignment of orthology: back to phylogenetics?,” Text, 2008, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760865/?tool=pubmed.	+	# “PLoS ONE: Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes.” http://www.plosone.org/article/fetchArticle.action?articleURI=info:doi/10.1371/journal.pone.0000383.

Darek Kedra: references

Darek Kedra — Mon, 07 Dec 2009 11:10:21 GMT

references

←Older revision		Revision as of 11:10, 7 December 2009
Line 18:		Line 18:
	==Orthologues retrival==		==Orthologues retrival==
	* [http://orthomcl.cbil.upenn.edu/cgi-bin/OrthoMclWeb.cgi?rm=index OrthoMCL]		* [http://orthomcl.cbil.upenn.edu/cgi-bin/OrthoMclWeb.cgi?rm=index OrthoMCL]
		+
		+	=References=
		+	1. “Joining forces in the quest for orthologs,” Text, 2009, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768974/.
		+
		+	2. “Large-scale assignment of orthology: back to phylogenetics?,” Text, 2008, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760865/?tool=pubmed.

Darek Kedra: +category

Darek Kedra — Thu, 31 Jul 2008 14:33:52 GMT

+category

←Older revision		Revision as of 14:33, 31 July 2008
Line 18:		Line 18:
	==Orthologues retrival==		==Orthologues retrival==
	* [http://orthomcl.cbil.upenn.edu/cgi-bin/OrthoMclWeb.cgi?rm=index OrthoMCL]		* [http://orthomcl.cbil.upenn.edu/cgi-bin/OrthoMclWeb.cgi?rm=index OrthoMCL]
		+
		+
		+
		+
		+	[[Category:Protocol]]
		+	[[Category:In silico]]
		+	[[Category:Sequence analysis]]

Darek Kedra: lit

Darek Kedra — Thu, 17 Jul 2008 10:35:34 GMT

lit

←Older revision		Revision as of 10:35, 17 July 2008
Line 10:		Line 10:
	* [http://orthomcl.org/cgi-bin/OrthoMclWeb.cgi OrthoMCL] TribeMCL		* [http://orthomcl.org/cgi-bin/OrthoMclWeb.cgi OrthoMCL] TribeMCL
	* [http://cd-hit.org/ CD-HIT] fast clustering of proteins and i.e. ESTs.		* [http://cd-hit.org/ CD-HIT] fast clustering of proteins and i.e. ESTs.
-	* [http://phylogenomics.berkeley.edu/cgi-bin/flowerpower/input_flowerpower.py FlowerPower]	+	* [http://phylogenomics.berkeley.edu/cgi-bin/flowerpower/input_flowerpower.py FlowerPower] protein homology clustering algorithm, similar to PSI-BLAST in its iterated approach to alignment, profile construction, and homolog identification, but with distinct differences.
-	~~FlowerPower is a~~ protein homology clustering algorithm, similar to PSI-BLAST in its iterated approach to alignment, profile construction, and homolog identification, but with distinct differences.	+

	* [http://www.ebi.ac.uk/~guy/exonerate/exonerate.man.html Exonerate] tool from sanger		* [http://www.ebi.ac.uk/~guy/exonerate/exonerate.man.html Exonerate] tool from sanger

Darek Kedra: init

Darek Kedra — Thu, 17 Jul 2008 10:34:58 GMT

init

New page

=Protein orthologues=

For simple orthologue retrieval in vertebrates use [http://www.ensembl.org/index.html Ensembl]. Each gene has there a list of best reciprocal hits in other species.

Review paper: [http://www.plosone.org/article/fetchArticle.action?articleURI=info:doi/10.1371/journal.pone.0000383 PLOS One 2007]

For clustering multiple sequences:

* [http://inparanoid.sbc.su.se/ Inparanoid]
* [http://orthomcl.org/cgi-bin/OrthoMclWeb.cgi OrthoMCL] TribeMCL
* [http://cd-hit.org/ CD-HIT] fast clustering of proteins and i.e. ESTs.
* [http://phylogenomics.berkeley.edu/cgi-bin/flowerpower/input_flowerpower.py FlowerPower]
FlowerPower is a protein homology clustering algorithm, similar to PSI-BLAST in its iterated approach to alignment, profile construction, and homolog identification, but with distinct differences.

* [http://www.ebi.ac.uk/~guy/exonerate/exonerate.man.html Exonerate] tool from sanger

==Orthologues retrival==
* [http://orthomcl.cbil.upenn.edu/cgi-bin/OrthoMclWeb.cgi?rm=index OrthoMCL]