protr (version 1.7-4)

twoSeqSim: 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
)

Value

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

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.

Author

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

if (FALSE) {

# 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)
}