[ssml] Re: [BiO BB] orthologs vs in-paralogs

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Fri Sep 5 02:38:56 EDT 2003

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?

Good question! Maby someone on the sequence searching mailing list can help answer,


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'?


> Best regards,
> Phil
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