twoSeqSim: Protein Sequence Alignment for Two Protein Sequences

In protr: Generating Various Numerical Representation Schemes for Protein Sequences

Protein Sequence Alignment for Two Protein Sequences

Description

Sequence alignment between two protein sequences.

Usage

twoSeqSim(
  seq1,
  seq2,
  type = "local",
  submat = "BLOSUM62",
  gap.opening = 10,
  gap.extension = 4
)

Arguments

seq1	Character string, containing one protein sequence.
seq2	Character string, containing another protein sequence.
type	Type of alignment, default is "local", could be "global" or "local", where "global" represents Needleman-Wunsch global alignment; "local" represents Smith-Waterman local alignment.
submat	Substitution matrix, default is "BLOSUM62", can be one of "BLOSUM45", "BLOSUM50", "BLOSUM62", "BLOSUM80", "BLOSUM100", "PAM30", "PAM40", "PAM70", "PAM120", or "PAM250".
gap.opening	The cost required to open a gap of any length in the alignment. Defaults to 10.
gap.extension	The cost to extend the length of an existing gap by 1. Defaults to 4.

Value

A Biostrings object containing the alignment scores and other alignment information.

Author(s)

Nan Xiao <https://nanx.me>

See Also

See parSeqSim for paralleled pairwise protein similarity calculation based on sequence alignment. See twoGOSim for calculating the GO semantic similarity between two groups of GO terms or two Entrez gene IDs.

Examples

## Not run: 

# Be careful when testing this since it involves sequence alignment
# and might produce unpredictable results in some environments

library("Biostrings")

s1 <- readFASTA(system.file("protseq/P00750.fasta", package = "protr"))[[1]]
s2 <- readFASTA(system.file("protseq/P10323.fasta", package = "protr"))[[1]]
seqalign <- twoSeqSim(s1, s2)
summary(seqalign)
score(seqalign)

## End(Not run)

protr documentation built on Sept. 12, 2024, 6:44 a.m.