Brian Foley wrote:
> I am looking for an automated (or even semi-autimated)
> method for generating a multiple sequence alignment of something
> like 6,000 sequences, all of them > 80% identical to one another.
> I wish to align the envelope gene (or portions there-of)
> which have been sequenced from the Human Immunodeficiency Virus
> type 1 or types 1 and 2. A BLAST search against the nr dataset
> provided by NCBI reveals that there are several thousand HIV
> env sequences in the database today.
Aligning this number of sequences shouldn't be a problem for most
multiple alignment programs since the sequences are very similar to
each other. However, you may need to redimension
arrays to cope with 6,000 sequences.
My alignment program AMPS ought to cope with this in
"single order" mode (see our WWW and ftp site below for on-line
manual and download instructions), though I have never tried to align
this many sequences!
Geoffrey J. Barton, Laboratory of Molecular Biophysics, University of
Rex Richards Building, South Parks Road, Oxford OX1 3QU, U.K.
mailto:gjb at bioch.ox.ac.uk, Tel: +44 1865 275368, Fax: +44 1865 510454,