Massive Multiple Sequence Alignment tools?

higgins at ebi.ac.uk higgins at ebi.ac.uk
Tue Apr 30 07:39:00 EST 1996

In article <31849227.794B at bioch.ox.ac.uk>, Geoff Barton <gjb at bioch.ox.ac.uk> writes:
> 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!
> Geoff.

Yes, Geoff's program (AMPS) is worth a try for this.  Clustal can do it in 
principle if you redimension it but is likely to take a LONG time and I am sure
you will blow it up somewhere if you try.   The time will get used up just
comparing all the sequences to each other in order to make a guide tree.
6000 sequences to be self compared will require 15,000,000 comparisons
and then you will need a few days cpu to make the tree.

I hope you have a good idea what you want to do with the sequences when
they are aligned :-).  It will take a long time to print out if you wish
to eye-ball it (or you will need a VERY small font on a VERY big monitor).

Des Higgins
EMBL/EBI, Hinxton.

> -- 
> Geoffrey J. Barton, Laboratory of Molecular Biophysics, University of
> Oxford, 
> 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, 
> ftp://geoff.biop.ox.ac.uk, http://geoff.biop.ox.ac.uk

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