localAligmentNucleotideSequence: Finds the optimal local nucleotide sequence aligment with...

In frosinastojanovska/Bioinformatics: A collection of functions for Bioinformatics

Description

Finds the optimal local nucleotide sequence aligment with Smith-Waterman algorithm and BLOSUM50 as score matrix.

Usage

localAligmentNucleotideSequence(sequence1, sequence2, gapPenalty, matchingScore,
  unmatchingScore)

Arguments

sequence1	First vector with characters indicating some of DNA nucleotides.
sequence2	Second vector with characters indicating some of DNA nucleotides.
gapPenalty	A number indicating the gap penalty value.
matchingScore	A number indicating the value for matching nucleotides.
unmatchingScore	A number indicating the value for unmatching nucleotides.

Value

List containing the score, the resulting aligned sequences and the matrix of aligment.

Examples

localAligmentNucleotideSequence(c("A","C","A","C","A","C","T","A"), c("A","G","C","A","C","A","C","A"), 1, 2, -1)

frosinastojanovska/Bioinformatics documentation built on May 16, 2019, 3:32 p.m.