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

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

email : cjfields at jove.acs.unt.edu
"Giving money and power to government is like giving
 whiskey and car keys to teenage boys"
				-P. J. O'Rourke

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.


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
ftp://geoff.biop.ox.ac.uk, http://geoff.biop.ox.ac.uk

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