Description Usage Arguments Details Value Author(s) See Also Examples
Parallellized DNA/RNA Sequence Similarity Calculation based on Sequence Alignment
1 |
dnalist |
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 DNA/RNA sequence similarity based on sequence alignment.
A n
x n
similarity matrix.
Min-feng Zhu <wind2zhu@163.com>
See twoSeqSim
for DNA/RNA sequence alignment
for two DNA/RNA sequences. See parGOSim
for
DNA/RNA similarity calculation based on
Gene Ontology (GO) semantic similarity.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | # Be careful when testing this since it involves parallelisation
# and might produce unpredictable results in some environments
require(Biostrings)
require(foreach)
require(doParallel)
s1 = readFASTA(system.file('dnaseq/hs.fasta', package = 'rDNA'))[[1]]
s2 = readFASTA(system.file('dnaseq/hs.fasta', package = 'rDNA'))[[2]]
s3 = readFASTA(system.file('dnaseq/hs.fasta', package = 'rDNA'))[[3]]
s4 = readFASTA(system.file('dnaseq/hs.fasta', package = 'rDNA'))[[4]]
s5 = readFASTA(system.file('dnaseq/hs.fasta', package = 'rDNA'))[[5]]
plist = list(s1, s2, s3, s4, s5)
psimmat = parSeqSim(plist, cores = 2, type = 'local', submat = 'BLOSUM62')
print(psimmat)
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