calcParProtSeqSim: Parallellized Protein Sequence Similarity Calculation based...

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/904-calcProtSeqSim.R

Description

Parallellized Protein Sequence Similarity Calculation based on Sequence Alignment

Usage

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calcParProtSeqSim(protlist, cores = 2, type = "local",
  submat = "BLOSUM62")

Arguments

protlist

A length n list containing n protein sequences, each component of the list is a character string, storing one protein sequence. Unknown sequences should be represented as ''.

cores

Integer. The number of CPU cores to use for parallel execution, default is 2. Users could use the detectCores() function in the parallel package to see how many cores they could use.

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', could be one of 'BLOSUM45', 'BLOSUM50', 'BLOSUM62', 'BLOSUM80', 'BLOSUM100', 'PAM30', 'PAM40', 'PAM70', 'PAM120', 'PAM250'.

Details

This function implemented the parallellized version for calculating protein sequence similarity based on sequence alignment.

Value

A n x n similarity matrix.

Author(s)

Min-feng Zhu <wind2zhu@163.com>, Nan Xiao <http://r2s.name>

See Also

See calcTwoProtSeqSim for protein sequence alignment for two protein sequences. See calcParProtGOSim for protein similarity calculation based on Gene Ontology (GO) semantic similarity.

Examples

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s1 = readFASTA(system.file('protseq/P00750.fasta', package = 'BioMedR'))[[1]]
s2 = readFASTA(system.file('protseq/P08218.fasta', package = 'BioMedR'))[[1]]
s3 = readFASTA(system.file('protseq/P10323.fasta', package = 'BioMedR'))[[1]]
s4 = readFASTA(system.file('protseq/P20160.fasta', package = 'BioMedR'))[[1]]
s5 = readFASTA(system.file('protseq/Q9NZP8.fasta', package = 'BioMedR'))[[1]]
plist = list(s1, s2, s3, s4, s5)
psimmat = calcParProtSeqSim(plist, cores = 2, type = 'local', submat = 'BLOSUM62')

BioMedR documentation built on Nov. 17, 2017, 10:08 a.m.