SWalgorithm: Smith-Watermam Algorithm

In ygu427/seqAlign: sequence alignment

Description

Implement the Smith-Waterman Algorithm to produce local pairwise sequence alignment

Usage

SWalgorithm(seq1, seq2, subMatrix, gapOpening = 8, gapExtension = 8)

Arguments

seq1	input the first sequence
seq2	input the second sequence
subMatrix	substitution matrix for protein sequence alignment or score matrix for DNA/RNA sequence alignment
gapOpening	the penalty for opening a gap in the alignment
gapExtension	the penalty for extending a gap by one residue

Value

path	the optimal path in pairwaise sequence alignment
fMatrix	the score table used in pairwise sequence alignment to determine optimal path
bestScore	the best score(s) in local pairwise sequence alignemtn to start the track back

Author(s)

Yu Gu

References

Durbin, Richard, Sean R. Eddy, Anders Krogh, and Graeme Mitchison. Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge university press, 1998.

ygu427/seqAlign documentation built on May 4, 2019, 2:33 p.m.