Dear all,
I need to make a spreadsheet with a list of all s.cerevisiae genes and their orthologues in Yarrowia lipolytica. I know i can do things like that in ensembl, but they do not have informations about y. lipolytica there. Is there any other database that have a function of finding orthologus genes?
Thank you for your answers! Martin
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martin.kavscek •
OMA is another good database of orthologs and contains information about both organisms omabrowser.org). You can also calculate yourself the orthologs, for instance with the Inparanoid algorithm which is available as a standalone application (http://inparanoid.sbc.su.se/).
For more information about ortholog databases and predictions, you may have a look (or instance) at Alexeyenko, A., Lindberg, J., Pérez-Bercoff, Å., & Sonnhammer, E. L. L. (2006). Overview and comparison of ortholog databases. Drug Discovery Today: Technologies, 3(2), 137–143. doi:10.1016/j.ddtec.2006.06.002 and Altenhoff AM, Dessimoz C (2009) Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods. PLoS Comput Biol 5(1): e1000262.
OMA is also available as stand-alone program: http://omabrowser.org/standalone
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Christophe Dessimoz
Since you are interested in yeast you can use SYNERGY, the orthogroups they define are based on reconstruction of the genes on the phylogenetic tree and should be accurate. The paper is here: http://bioinformatics.oxfordjournals.org/content/23/13/i549.full
With two closely related yeast genomes there should be a lot of synteny between the two. If there are no well defined GFF files for Yarrowia lipolytica, you should be able transfer gene models to a well constructed map of genome synteny. There are multiple methods to do this.
Have you tried something like OrthoMCL?
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