> This is a good question, please drop me a note if you guys get some answers. > > For all I know, besides the homolog part, the key difference is that ortholog is > same function in different species, while paralog is different function in same > species. Yup, I know this definition, but it doesn't address the idea or redundancy within a genome. This is (apparently) a big issue for functional genomics. Cheers > Please keep me posted! > Thanks! > haibo > //cheers > > Quoting Dan Bolser <dmb at mrc-dunn.cam.ac.uk>: > >> Phil Luo said: >> > Dear all, >> > >> > As we know ,there are two kinds of homolog, ortholog and paralog. >> Genes in two >> > species that have directly evolved from a single gene in the last >> common ancestor >> > are called orthologs. A set of homologous genes that have diverged >> from each other >> > as a consequence of genetic duplication are called paralogs. Sometime >> those >> > paralogs which arose from a duplication after the speciation event are >> called >> > in-paralogs. >> > >> > My question is how to distinguish the in-paralogs from orthologs. >> Which one is >> > supposed to be more similar, in-paralogs or orthologs? >> >> Hi, >> Good question! Maby someone on the sequence searching mailing list can help >> answer, >> >> http://bioinformatics.org/mailman/listinfo/ssml-general >> >> >> I know of some work trying to uncover 'lineage specific gene expansion' by >> Eugene >> Koonin (sp?) at the NCBI. That sounds a bit like the in-paralogues you describe. >> Also he and coworkers define an algorithm for predicting orthologous pairs, >> simply >> 'best hits' between genome 1 and 2. >> >> Although I understand the definition of orthology and paralogy, I find the >> concepts >> a bit confusing. I don't know what information you loose by simply talking about >> gene families, and ignoring the within / between genome distinction. >> >> At some level does't ortholog mean 'same gene', and paralog mean 'copy'? >> >> Cheers, >> >> > Best regards, >> > Phil >> > >> > >> > --------------------------------- >> > Do you Yahoo!? >> > Yahoo! SiteBuilder - Free, easy-to-use web site design software >> >> >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> > > > > ========================================================= > Haibo Zhang, PhD student > Computational Biology, NJIT & Rutgers University > Center for Applied Genomics, PHRI > http://afs13.njit.edu/~hz5