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