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find multiple matching subsegments in two sequences

This is William Pearson's lalign program. A manual page for this program is available here. The lalign program implements the algorithm of Huang and Miller, published in Adv. Appl. Math. (1991) 12:337-357.

This program is part of the FASTA package of sequence analysis program.


Usage: Paste your two sequences in one of the supported formats into the sequence fields below
and press the "Run lalign" button.
Make sure that both format buttons (next to the sequence fields) shows the correct formats
Choose the alignment method: local (default) global global without end-gap penalty
Number of reported sub-alignments:
Scoring matrix:
Opening gap penalty : (default -14)
Extending gap penalty : (default -4)
First sequence title (optional):
Input sequence format
1st Query sequence:
or ID or AC or GI
(see above for valid formats)
Second sequence title (optional):
Input sequence format
2nd Query sequence:
or ID or AC or GI
(see above for valid formats)