[BiO BB] Aligning sequence from pdb to an established MSA

Dan Bolser dan.bolser at gmail.com
Fri Aug 31 15:56:55 EDT 2007


On 31/08/2007, Mike Marchywka <marchywka at hotmail.com> wrote:
>
>
> Do you have a link to any HMM code downloads? I've been using clustalw but
> looking for other stuff. I think someone posted links before but I don't
> have
> any handy.



You can grab HMMER here http://hmmer.janelia.org/


HMMER does not currently use any structural information to align sequences
(although it could in principle). SAM uses various predicted structural
descriptors to improve homologue detection, but I am not sure what the
release/development status of that program is.

I seem to remember that performing explicit structural alignments to
generate a seed sequence for an iterative HMM building job actually performs
slightly worse at homologue detection than just using a clustalw alignment
as the seed. The theory being that because the HMM is iteratively built it
doesn't really matter that much how good the seed alignment is. I think that
finding was described in the papers describing the SUPERFAMILY database of
HMM's.

HMMER was just one idea for the solution to the question given an alignment,
how do I align a sequence to the alignment. You can do that with the
'hmmalign' app. For example here;

http://bioweb.pasteur.fr/seqanal/interfaces/hmmalign.html


I don't know if this is the best / easiest solution.



Thanks.
>
>
> Mike Marchywka
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>
>
>
>
> >From: "Dan Bolser" <dan.bolser at gmail.com>
> >Reply-To: "General Forum at Bioinformatics.Org "
> ><bio_bulletin_board at bioinformatics.org>
> >To: "General Forum at Bioinformatics.Org"
> >< bio_bulletin_board at bioinformatics.org>
> >Subject: Re: [BiO BB] Aligning sequence from pdb to an established MSA
> >Date: Fri, 31 Aug 2007 18:31:40 +0200
> >
> >HMM like HMMER can do this.
> >
> >On 30/08/2007, Kai Ye <k.ye at lacdr.leidenuniv.nl> wrote:
> > >
> > > Dear all:
> > >
> > > Any idea about a linux program to align the sequence extracted from
> pdb
> > > with
> > > an established MSA. In the MSA there may or may not be a sequence
> > > identical
> > > to the one from pdb.
> > >
> > > Thanks in advance!
> > >
> > > Kai
> > >
> > >
> > >
> > > _______________________________________________
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> >
> >
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