Pairwise alignment of 200,000 and 20,000 bp sequences

Ashok Aiyar aiyar at ebv.oncology.wisc.edu
Thu Jun 12 16:47:56 EST 1997

On Thu, 12 Jun 1997 14:19:36 -0400,
Max V Myakishev (max at scientist.com) wrote:
>I am looking for the tool to perform 
>pairwise alignment of 200,000 and 20,000 bp sequences.
>Preferable computer platforms: WWW > PC > Mac > UNIX.
>I already tried many programs and most of them 
>are limited by the input sequence size 32000.

Get the FASTA source from ftp.virginia.edu.  It is trivial to modify 
the source for the ALIGN program within the FASTA package to use 
input sequences of any desired length.  Note that Bill Pearson doesn't 
recommend that this be done - as smaller alignments will likely be 
missed.  However I regularly use ALIGN for pairwise alignments of 
sequences that are in the range of 100 - 200 kb.

Ashok Aiyar, Ph.D.
McArdle Laboratory for Cancer Research
aiyar at ebv.oncology.wisc.edu

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