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

[Mensur Dlakic]

Hi,

This question will always be debated, but there are still things that most 
people agree on. I suggest the following two articles that deal with 
automatic clustering of orthologs and paralogs.

1: 
<http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11836216&dopt=Abstract>Storm 
CE, Sonnhammer EL.
<http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11836216&dopt=Abstract&itool=iconabstr>4930dab.jpg 
Automated ortholog inference from phylogenetic trees and calculation of 
orthology reliability.
Bioinformatics. 2002 Jan;18(1):92-9.
PMID: 11836216 [PubMed - indexed for MEDLINE]
2: 
<http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11743721&dopt=Abstract>Remm 
M, Storm CE, Sonnhammer EL.
<http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11743721&dopt=Abstract&itool=iconabstr>4930e55.jpg 
Automatic clustering of orthologs and in-paralogs from pairwise species 
comparisons.
J Mol Biol. 2001 Dec 14;314(5):1041-52.
PMID: 11743721 [PubMed - indexed for MEDLINE]


At 07:38 AM 9/5/2003 +0100, you wrote:
>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?

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| Mensur Dlakic, Ph.D.              | Tel: (406) 994-2903                |
| Department of Microbiology        | Fax: (406) 994-4926                |
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