SSEARCH
SSEARCH. This program performs a rigorous Smith-Waterman alignment between a protein sequence and another protein sequence or a protein database. SSearch uses William Pearson's implementation of the method of Smith and Waterman (Advances in Applied Mathematics 2; 482-489 (1981)) to search for similarities between one sequence (the query) and any group of sequences of the same type (nucleic acid or protein) as the query sequence. Part of the Fasta Family. See: Pearson WR, Lipman DJ (1988) "Improved tools for biological sequence comparison." PNAS USA. 85(8):2444-8.
Manual: http://www.med.nyu.edu/rcr/rcr/fastaman.html
INPUT = Nucleic Acid or Protein sequence files in fasta format.
TEST INPUT FILES
Input file: ssearch_in.txt
TEST OUTPUT FILES
Output file: ssearch_out.txt
