calcParProtSeqSim {Rcpi} | R Documentation |
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 |
This function implemented the parallellized version for calculating protein sequence similarity based on sequence alignment.
A n
x n
similarity matrix.
Nan Xiao <https://nanx.me>
See calcTwoProtSeqSim
for protein sequence alignment
for two protein sequences. See calcParProtGOSim
for
protein similarity calculation based on
Gene Ontology (GO) semantic similarity.
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) psimmat = calcParProtSeqSim(plist, cores = 2, type = 'local', submat = 'BLOSUM62') print(psimmat)