I have a set of proteins from organism X. I want to estimate the conservancy of these proteins across 9 other organisms. I did the orthology search but it gives the counts weather the protein ortholog is present in other organism or not. Further the orthology search become more complicated as the inparalogs and isoforms from other species grouped in same cluster. So, I am looking for the better way to estimate the conservancy (score) for proteins in the other genome..
HI, you can try Rate4Site, it is a program for detecting conserved amino-acid sites by computing the relative evolutionary rate for each site in the multiple sequence alignment (MSA). More information, pls visit websie: http://www.tau.ac.il/~itaymay/cp/rate4site.html
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Hi, I ever encountered the same problem when I do transcriptome analysis. It really can be complicated. you could compare the conservation domain of the proteins among all the genomes to determine the protein conservancy, no matter how they are generated (duplication or splicing). If you could distinguish between the isoforms and paralogs, I think you can throw away the isoforms since they are the alternative splicing result (splicing is an common event for most eukaryote genes). I don't know whether this helps or not. just for your reference.
If the genome you are looking at is a publicly available genome then you can go to SUPERFAMILY and use the extensive comparative genomics tools there. E.g. for Kerosene fungus you have:
http://supfam.org/SUPERFAMILY/cgi-bin/unusual_list.cgi?set=Custom+set+1;sortgens=Fm1,lz,b7;genome=EPt;listtype=sf
comparing it to other Leotiomycetes, and you also can compare families and ontologies
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