do the local pairwise sequence alignment via the smith-waterman

align.smith_waterman {bioseq.blast}

R Documentation

do the local pairwise sequence alignment via the smith-waterman

Description

algorithm

Usage

align.smith_waterman(query, ref,
    blosum = NULL);

Arguments

query

a FastaSeq sequence object of the query sequence. [as FastaSeq]

ref

a FastaSeq sequence object of the reference subject sequence. [as FastaSeq]

blosum

the amino acid substitution score matrix for the alignment, which can be created by the blosum api in this package module. If this parameter is nothing, then the default Blosum-62 score matrix will be used. [as Blosum]

Authors

seqtoolkit

Value

a SmithWaterman local alignment result object, from which the high score region details can be extracted via the HSP api.

clr value class

SmithWaterman

[Package bioseq.blast version 1.0.0.0 Index]