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[Molecular-evolution] Re: Quantitating the degree of conservation

Siby Philip via mol-evol%40net.bio.net (by sibyphilips from gmail.com)
Mon Feb 1 08:54:54 EST 2010


The UCSC genome browser database: update 2010
Nucleic Acids Research, doi:10.1093/nar/gkp939

..I think they have implemented the phyloP conservation scores...though I am
not sure about it since I have not browsed it yet...however if they have
implemented the phyloP scores then you will get the amount of conservation
among the species for genes and also for sites I think,
thanks,
Siby


On Mon, Feb 1, 2010 at 1:39 AM, Don Gilbert <gilbertd from bio.indiana.edu>wrote:

> THe various protein databases do clustering of genes.
> You might want to use the number of species or gene copies in a gene
> cluster
> as a measure of convervation.  E.g. Uniprot's UniRef data set.
>
> http://www.uniprot.org/uniref/?query=histone&sort=score
>        (max 5,345 genes at 50% identity)
> versus
> http://www.uniprot.org/uniref/?query=obp&sort=score
>        (max 23 genes at 50% id)
>
> -- Don
>
> On 2010-01-27, Sidney Cambridge <cambridge from ana.uni-heidelberg.de> wrote:
> >
> > Dear all,
> >
> > I hope my question is not too trivial....
> > I am looking for a quantitative measure of the degree of genetic
> > conservation - basically attaching a high value to highly conserved
> > genes such as histones and low values to genes that are not very
> > conserved. Ideally there would be a database for all genes of the
> > mouse or human genome with a 'conservation' value for each gene.
> >
> > Does something like this exist ?
> >
> > Thank you very much in advance !
> >
> > Best,
> > Sidney
>
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-- 
Siby Philip
Doctoral Research Fellow,
Laboratory of Ecotoxicology, genomics and Evolution,
Centro Interdisciplinar de Investigação Marinha e Ambiental,
Rua dos Bragas,
Porto,
Portugal.

and also at

http://crgkerala.org/siby.html
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