R/704-calcProtSeqSim.R
calcParProtSeqSim.Rd
Parallellized Protein Sequence Similarity Calculation based on Sequence Alignment
calcParProtSeqSim(protlist, cores = 2, type = "local", submat = "BLOSUM62")
protlist | A length |
---|---|
cores | Integer. The number of CPU cores to use for parallel execution,
default is |
type | Type of alignment, default is |
submat | Substitution matrix, default is |
A n
x n
similarity matrix.
This function implemented the parallellized version for calculating protein sequence similarity based on sequence alignment.
See calcTwoProtSeqSim
for protein sequence alignment
for two protein sequences. See calcParProtGOSim
for
protein similarity calculation based on
Gene Ontology (GO) semantic similarity.
# NOT RUN { s1 = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]] s2 = readFASTA(system.file('protseq/P08218.fasta', package = 'Rcpi'))[[1]] s3 = readFASTA(system.file('protseq/P10323.fasta', package = 'Rcpi'))[[1]] s4 = readFASTA(system.file('protseq/P20160.fasta', package = 'Rcpi'))[[1]] s5 = readFASTA(system.file('protseq/Q9NZP8.fasta', package = 'Rcpi'))[[1]] plist = list(s1, s2, s3, s4, s5) # }# NOT RUN { psimmat = calcParProtSeqSim(plist, cores = 2, type = 'local', submat = 'BLOSUM62') print(psimmat) # }