clustal protein alignment with >50 sequences?

Chris Fields cjfields at jove.acs.unt.edu
Fri Sep 26 01:38:02 EST 1997


ClustalW works very well.  I used version 1.6 to align 60 rRNA sequences
(~1500 bp apiece) and it worked well.  I did run into a problem in exceeding
the maximum length, but I believe Des Higgins posted recently that the newer
version (1.7) has no maximum limit except for available memory.  A version
for Windows and Mac also exists, called ClustalX, and also works very well.

Versions of Clustal are found at the IUBIO Archive and in the Biocatalog at
EMBL.

Cheers,
--
C. J. Fields
Graduate Student, Dept. of Biological Sciences
The University of North Texas
Denton, TX

email : cjfields at jove.acs.unt.edu
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Geoff Barton wrote in article <3428D8E5.2C67 at bioch.ox.ac.uk>...

Ashok Aiyar wrote:
>
> On Sat, 13 Sep 1997 00:46:11 GMT,
> davesmith at bioch.tamu.edu (davesmith at bioch.tamu.edu) wrote:
> >We have 51 different phage and chromosomal sequences of the protein we
> >study.  None are more than 200 residues in length.  After an
> >exhaustive search of the web, we've been unable to find a program that
> >will line up more than 25 proteins at once.  Does anyone know of a way
> >to line these up and generate a dendrogram or "family tree" with such
> >a large number of individual proteins?

I didn't see the original post for this, but if you are running
on a Unix workstation, you can also try AMPS.  See our ftp/web site
for details.

Geoff.

--------------------
Geoffrey J. Barton, Laboratory of Molecular Biophysics,
University of Oxford,
Rex Richards Building, South Parks Road, Oxford OX1 3QU, U.K.
mailto:geoff.barton at ox.ac.uk, Tel: +44 1865 275368, Fax: +44 1865
510454,
ftp://geoff.biop.ox.ac.uk, http://geoff.biop.ox.ac.uk






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