[BiO BB] how to compare biological distance between four proteins

[Pedro Fernandes]

Hello again

If you are looking for (known) functional properties you should use multiple
alignments tuned so that you align motifs that you know that are related with
known functions better than other parts of the protein sequences.

You may know those motifs, because you may know protein domains or motifs that
are associated with each function. You may also generate motifs for that
purpose, artificially. finally, you may work on the conservation and select the
bits of sequence that may have had a common ancestor where that particular
function was found.

Pedro

-- 
Pedro Fernandes
Centro Português de Bioinformática
Instituto Gulbenkian de Ciência
Apartado 14
2781 OEIRAS
PORTUGAL
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Quoting Xue Li <me.lixue at gmail.com>:

> Sorry for the confusion.
>
> By "Biological distance" I mean functional similarity.
>
> Thanks.
>
> Li
>
> On Wed, Jun 4, 2008 at 3:30 PM, Iddo Friedberg <idoerg at gmail.com> wrote:
>
> > What is "Biological distance"?
> >
> > On Wed, Jun 4, 2008 at 9:12 AM, Xue Li <me.lixue at gmail.com> wrote:
> >
> > > Hello all,
> > >
> > > I have four proteins. 1AAI:A 1RZO:C 1UQ5:A 1UQ4:A
> > >
> > > Only 1RZO:C,  1UQ5:A and 1UQ4:A have Uniprot accession No.
> > >
> > > 1RZO:C is P06750
> > > 1UQ5:A and 1UQ4:A are P02879
> > >
> > > I am interested in comparing biological distance of 1AAI:A with the other
> > > three. Would some one please tell me how to do that?
> > >
> > > Thanks a lot.
> > >
> > > --
> > > Xue, Li
> > > Bioinformatics and Computational Biology program @ ISU
> > > Ames, IA 50010
> > > 515-450-7183
> > > _______________________________________________
> > > BBB mailing list
> > > BBB at bioinformatics.org
> > > http://www.bioinformatics.org/mailman/listinfo/bbb
> > >
> >
> >
> >
> > --
> >
> > Iddo Friedberg, Ph.D.
> > CALIT2, mail code 0440
> > University of California, San Diego
> > 9500 Gilman Drive
> > La Jolla, CA 92093-0440, USA
> > T: +1 (858) 534-0570
> > T: +1 (858) 646-3100 x3516
> > http://iddo-friedberg.org
> > _______________________________________________
> > BBB mailing list
> > BBB at bioinformatics.org
> > http://www.bioinformatics.org/mailman/listinfo/bbb
> >
>
>
>
> --
> Xue, Li
> Bioinformatics and Computational Biology program @ ISU
> Ames, IA 50010
> 515-450-7183
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>