File	Date	Author	Commit
example	2012-01-30	Isaac Turner	[3c85e6] Removed redundant lines leftover from Needleman...
perl	2012-10-07	Isaac Turner	[58caba] commit.mesg
LICENSE	2012-01-27	Isaac Turner	[a0719e] Changed email address & copyright date in LICEN...
Makefile	2012-10-07	Isaac Turner	[58caba] commit.mesg
README	2012-01-21	Isaac Turner	[034789] Improved file handling
smith_waterman.c	2012-10-07	Isaac Turner	[58caba] commit.mesg
smith_waterman.h	2012-10-07	Isaac Turner	[58caba] commit.mesg
sw_cmdline.c	2012-10-07	Isaac Turner	[58caba] commit.mesg

Read Me

Smith-Waterman optimal local alignment
Isaac Turner
turner.isaac@gmail.com

== Build ==

$ make

or

$ make DEBUG=1

== Run ==

$ smith_waterman ACCGATA CCGT

To get a list of options/help:

$ smith_waterman

== Scoring systems ==

Proteins:
Query Length    Substitution Matrix   Gap Costs (gap_open,gap_extend)
<35             PAM-30                (9,1)
35-50           PAM-70                (10,1)
50-85           BLOSUM-80             (10,1)
85              BLOSUM-62             (10,1)
[table from http://www.ncbi.nlm.nih.gov/blast/html/sub_matrix.html]

gap (of length N) penalty: gap_open + N*gap_extend

NCBI BLAST Quote:
Many nucleotide searches use a simple scoring system that consists of a "reward"
for a match and a "penalty" for a mismatch. The (absolute) reward/penalty ratio
should be increased as one looks at more divergent sequences. A ratio of 0.33
(1/-3) is appropriate for sequences that are about 99% conserved; a ratio of 0.5
(1/-2) is best for sequences that are 95% conserved; a ratio of about one (1/-1)
is best for sequences that are 75% conserved [1].
[from: http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#Reward-penalty]

NCBI Gap (open, extend) values:
-5, -2
-2, -2
-1, -2
-0, -2
-3, -1
-2, -1
-1, -1

Our default (for now) are:
gap_open/gap_extend: (-1,-1)
match/mismatch: (2,-2)

== Development ==

- No current goals - please suggest some!