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