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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| smith_waterman-0.2.3.tar.gz | 2012-04-25 | 44.1 kB | |
| README | 2012-01-22 | 1.4 kB | |
| smith_waterman-0.2.2.tar.gz | 2012-01-22 | 41.0 kB | |
| smith_waterman-0.2.1.tar.gz | 2012-01-21 | 40.6 kB | |
| Totals: 4 Items | 127.0 kB | 0 |
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!