align_sequences: Sequence Alignment

In SeqAlignR: Sequence Alignment and Visualization Tool

Sequence Alignment

Description

Performs sequence alignment on two sequences by a user specified alignment method. As of now, only the Needleman-Wunsch algorithm is supported.

Usage

align_sequences(seq1, seq2, d, mismatch, match, method = "needleman")

Arguments

seq1	First sequence to align.
seq2	Second sequence to align.
d	Gap penalty, should be negative.
mismatch	Mismatch penalty, should be negative.
match	Match score, should be positive.
method	Name of alignment algorithm. Currently only supports "needleman".

Value

Object of class alignment representing the alignment result. This object can be utilized with the plot.alignment function to visualize the alignment matrix and the print.alignment function to display alignments in the console.

References

For more details on the Needleman-Wunsch algorithm, see the wikipedia page.

Examples

seq1 <- "GCATGCG"
seq2 <- "GATTACA"
# Run the Needleman-Wunsch algorithm
align_sequences(seq1, seq2, d = -1, mismatch = -1, match = 1)

SeqAlignR documentation built on May 29, 2024, 10:09 a.m.