[BioC] protein orthologs

Stefanie Carola Gerstberger scg74 at cornell.edu
Thu Mar 24 03:28:33 CET 2011


Dear list,
I'm trying to retrieve protein orthologs for human proteins for the most common model organism (mouse,C.elegans,Drosophila,S.cerevisae,etc) such that for my work in human I can point other researchers to the appropriate homolog in other species.
 
I was first using Ensembl Compara through biomart (Genome Res. 2009 Feb;19(2):327-35. Epub 2008 Nov 24. EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.) to query those orthologs, 

but then I came across inparanoid as a second resource.(Nucleic Acids Res. 2010 Jan;38(Database issue):D196-203. Epub 2009 Nov 5. InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.) 

I also came across SIMAP as a protein homology resource (Nucleic Acids Res. 2010 Jan;38(Database issue):D223-6. Epub 2009 Nov 11. SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters.)  which was used for a S.cerevisae database MIPS.  

I'm not experienced at all in this area and reading the publications did not give me a good indication on which one is the better resource for ortholog relationships. What I noticed and did not like from inparanoid is that (at least the website) does not give any % identities (but I haven't checked the R package yet). 

I would like to know which protein orthology database is commonly accepted as a standard resource in the protein evolutionary field. 
What is commonly used as reference in protein evolution labs?
Can anyone give me advice on this?

Thanks,
Stefanie


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