SSEARCH:

Description: Perform a sequence similarity search against TC-DB with a query protein. SSEARCH performs a rigorous Smith-Waterman local alignment between a protein and a protein database. SSEARCH employs an exhaustive algorithm whereas BLAST and FASTA use a heuristic methodology. As a consequence SSEARCH is slower in comparison to either BLAST or FASTA, however what you lose in speed is regained in sensitivity.

Expect Cutoff: 0.0001 0.01 1 10 100 1000 Alignments: 5 10 50 100 200 Matrix: PAM20 PAM40 PAM120 PAM250 BLOSUM50 BLOSUM62 BLOSUM80 PHAT70 PHAT75 PHAT80 PHAT85 SLIM160
Gap Open Penalty: 0 5 8 11 14 17 20 Gap Extension Penalty: 0 1 2 5 10 Show Histogram: No Yes

Enter protein UniProt ID or FASTA sequence: