SSEARCH: Protein versus protein

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.

Matrix:
Gap Open Penalty: Gap Extension Penalty: Number of Shuffles:

Please enter the first protein sequence with FASTA format you want to analyze:

Please enter the second protein sequence with FASTA format you want to analyze:

If you have any questions please e-mail: Can Tran - can@ucsd.edu

SSEARCH version 3.4t20 Nov 10, 2002
TC-DB version 1.5 Feb 25, 2003

T. F. Smith and M. S. Waterman, (1981) J. Mol. Biol. 147:195-191
W.R. Pearson (1991) Genomics 11:635-650