smithwaterman(1) determine similar regions between two strings or nucleotide or protein sequences


smithwaterman [options] <reference sequence> <query sequence>


The Smith–Waterman algorithm performs local sequence alignment; that is, for determining similar regions between two strings or nucleotide or protein sequences. Instead of looking at the total sequence, the Smith–Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure.


-m, --match-score
the match score (default 10.0)
-n, --mismatch-score
the mismatch score (default -9.0)
-g, --gap-open-penalty
the gap open penalty (default 15.0)
-z, --entropy-gap-open-penalty
enable entropy scaling of the gap open penalty
-e, --gap-extend-penalty
the gap extend penalty (default 6.66)
-r, --repeat-gap-extend-penalty
use repeat information when generating gap extension penalties
-b, --bandwidth
bandwidth to use (default 0, or non-banded algorithm)
-p, --print-alignment
print out the alignment
-R, --reverse-complement
report the reverse-complement alignment if it scores better

When called with literal reference and query sequences, smithwaterman prints the cigar match positional string and the match position for the query sequence against the reference sequence.


This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.