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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 a=
m
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@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=3Dhistone&sort=3Dscore
>        (max 5,345 genes at 50% identity)
> versus
> http://www.uniprot.org/uniref/?query=3Dobp&sort=3Dscore
>        (max 23 genes at 50% id)
>
> -- Don
>
> On 2010-01-27, Sidney Cambridge <cambridge@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
>
> _______________________________________________
> Mol-evol mailing list
> Mol-evol@net.bio.net
> http://www.bio.net/biomail/listinfo/mol-evol
>



--=20
Siby Philip
Doctoral Research Fellow,
Laboratory of Ecotoxicology, genomics and Evolution,
Centro Interdisciplinar de Investiga=E7=E3o Marinha e Ambiental,
Rua dos Bragas,
Porto,
Portugal.

and also at

http://crgkerala.org/siby.html

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<span style=3D"font-family: sans-serif; font-size: medium;"><h2><span style=
=3D"font-size: small;"><font face=3D"&#39;comic sans ms&#39;, sans-serif">T=
he UCSC genome browser database: update 2010</font></span></h2>
<div><span style=3D"font-size: small;"><font face=3D"&#39;comic sans ms&#39=
;, sans-serif">Nucleic Acids Research, doi:10.1093/nar/gkp939</font></span>=
</div><div><font face=3D"&#39;comic sans ms&#39;, sans-serif"><span style=
=3D"font-size: small;"><br>

</span></font></div><div><span style=3D"font-size: small;"><font face=3D"&#=
39;comic sans ms&#39;, sans-serif">..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,</font>=
</span></div>
<div><span style=3D"font-size: small;"><font face=3D"&#39;comic sans ms&#39=
;, sans-serif">thanks,</font></span></div><div><span style=3D"font-size: sm=
all;"><font face=3D"&#39;comic sans ms&#39;, sans-serif">Siby</font></span>=
</div>
</span><br><br><div class=3D"gmail_quote">On Mon, Feb 1, 2010 at 1:39 AM, D=
on Gilbert <span dir=3D"ltr">&lt;<a href=3D"mailto:gilbertd@bio.indiana.edu=
">gilbertd@bio.indiana.edu</a>&gt;</span> wrote:<br><blockquote class=3D"gm=
ail_quote" style=3D"border-left: 1px solid rgb(204, 204, 204); margin: 0pt =
0pt 0pt 0.8ex; padding-left: 1ex;">
THe various protein databases do clustering of genes.<br>
You might want to use the number of species or gene copies in a gene cluste=
r<br>
as a measure of convervation. =A0E.g. Uniprot&#39;s UniRef data set.<br>
<br>
<a href=3D"http://www.uniprot.org/uniref/?query=3Dhistone&amp;sort=3Dscore"=
 target=3D"_blank">http://www.uniprot.org/uniref/?query=3Dhistone&amp;sort=
=3Dscore</a><br>
 =A0 =A0 =A0 =A0(max 5,345 genes at 50% identity)<br>
versus<br>
<a href=3D"http://www.uniprot.org/uniref/?query=3Dobp&amp;sort=3Dscore" tar=
get=3D"_blank">http://www.uniprot.org/uniref/?query=3Dobp&amp;sort=3Dscore<=
/a><br>
 =A0 =A0 =A0 =A0(max 23 genes at 50% id)<br>
<br>
-- Don<br>
<br>
On 2010-01-27, Sidney Cambridge &lt;<a href=3D"mailto:cambridge@ana.uni-hei=
delberg.de">cambridge@ana.uni-heidelberg.de</a>&gt; wrote:<br>
&gt;<br>
&gt; Dear all,<br>
&gt;<br>
&gt; I hope my question is not too trivial....<br>
&gt; I am looking for a quantitative measure of the degree of genetic<br>
&gt; conservation - basically attaching a high value to highly conserved<br=
>
&gt; genes such as histones and low values to genes that are not very<br>
&gt; conserved. Ideally there would be a database for all genes of the<br>
&gt; mouse or human genome with a &#39;conservation&#39; value for each gen=
e.<br>
&gt;<br>
&gt; Does something like this exist ?<br>
&gt;<br>
&gt; Thank you very much in advance !<br>
&gt;<br>
&gt; Best,<br>
&gt; Sidney<br>
<br>
_______________________________________________<br>
Mol-evol mailing list<br>
<a href=3D"mailto:Mol-evol@net.bio.net">Mol-evol@net.bio.net</a><br>
<a href=3D"http://www.bio.net/biomail/listinfo/mol-evol" target=3D"_blank">=
http://www.bio.net/biomail/listinfo/mol-evol</a><br>
</blockquote></div><br><br clear=3D"all"><br>-- <br>Siby Philip<br>Doctoral=
 Research Fellow,<br>Laboratory of Ecotoxicology, genomics and Evolution,<b=
r>Centro Interdisciplinar de Investiga=E7=E3o Marinha e Ambiental,<br>Rua d=
os Bragas,<br>
Porto,<br>Portugal.<br><br>and also at<br><br><a href=3D"http://crgkerala.o=
rg/siby.html">http://crgkerala.org/siby.html</a><br>

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