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

[Kevin Karplus]

hz5 at njit.edu (haibo) wrote

> 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.

That is a probable consequence of orthology and paralogy, not the
definition.  With ancient paralogs (such as hemoglobin and myoglobin),
it is a useful property.  For recent paralogs (such as olfactory
receptors in rodents) it may not be that useful.

The definitions I've seen are all a little bit vague---they do not
handle well large gene families in which a lot of duplication and gene
elimination occur.  In many cases, even if the definition is clear, we
often have no way of determining whether or not two members of such a
family in different species are orthologs.  The closest matches
between the species may have arisen from different copies in the
ancestral species, and hence be paralogs rather than orthologs.


Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Professor of Computer Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
Affiliations for identification only.