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

frist at frist at
Mon Jun 16 09:40:00 EST 1997

Max V Myakishev 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.
> Thanks
> Max V Myakishev, Ph.D.
> Email: max at

If you want a dot-matrix style similarity comparison, D3HOM and D4HOM
in the Unix version of FSAP allow sequences of up to 750,000bp
(or greater if you recompile). Have a look at

(Note: the DOS versions of these programs do NOT allow
sequences >19,000).
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