GOOD SEQUENCE PROGRAM

Mark Israel misrael at grdb.csi.uottawa.ca
Tue May 3 11:46:30 EST 1994


In article <2q5psr$5f2 at netnews.upenn.edu>, Sean David Moore <smoore at mail.sas.upenn.edu> writes:

> I am looking for the name and/or location of the best sequence alignment
> program. [...]
>
> Is there even such a thing.?
>
> No responses as of the fifth post of this message were received except to
> ask for the response.

   Well, the following were described as "optimal"; so maybe they're 
the best.  Just a wild guess.

   (This was posted only a month ago.  Maybe it's time to start an 
FAQ file for this newsgroup.)

misrael at csi.uottawa.ca			Mark Israel

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Newsgroups: bionet.software
Subject: Re: Software for sequence alignment?
From: wrp at dayhoff.med.Virginia.EDU (William R. Pearson)
Organization: University of Virginia
Date: Thu, 31 Mar 1994 14:28:18 GMT
Message-ID: <CnJ9J6.5Kt at murdoch.acc.Virginia.EDU>

[...] The "align" program in the FASTA package (available from
"virginia.EDU" in "pub/fasta/fasta17.shar.Z") will produce optimal
global alignment with gaps for DNA and protein sequences. It aligns
only two sequences at once.  The only genuine optimal alignment
program for multiple sequences that I am aware of is "msa" (Lipman,
Altschul, and Kececioglu, (1989) PNAS 86:4412-4415) which is available
from ncbi.nlm.nih.gov.

Bill Pearson




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