问题
I have a large number of protein sequences in fasta format.
I want to get the pair-wise sequence similarity score for each pairs of the proteins.
Any package in R could be used to get the blast similarity score for protein sequences?
回答1:
As per Chase's suggestion, bioconductor is indeed the way to go and in particular the Biostrings package. To install the latter I would suggest installing the core bioconductor library as such:
source("http://bioconductor.org/biocLite.R")
biocLite()
This way you will cover all dependencies. Now, to align 2 protein sequences or any two sequences for that matter you will need to use pairwiseAlignment from Biostrings. Given a fasta protseq.fasta file of 2 sequences that looks like this:
>protein1
MYRALRLLARSRPLVRAPAAALASAPGLGGAAVPSFWPPNAAR
MASQNSFRIEYDTFGELKVPNDKYYGAQTVRSTMNFKIGGVTE
RMPTPVIKAFGILKRAAAEVNQDYGLDPKIANAIMKAADEVAE
GKLNDHFPLVVWQTGSGTQTNMNVNEVISNRAIEMLGGELGSK
IPVHPNDHVNKSQ
>protein2
MRSRPAGPALLLLLLFLGAAESVRRAQPPRRYTPDWPSLDSRP
LPAWFDEAKFGVFIHWGVFSVPAWGSEWFWWHWQGEGRPYQRF
MRDNYPPGFSYADFGPQFTARFFHPEEWADLFQAAGAKYVVLT
TKHHEGFTNW*
If you want to globally align these 2 sequences using lets say BLOSUM100 as your substitution matrix, 0 penalty for opening a gap and -5 for extending one then:
require("Biostrings")
data(BLOSUM100)
seqs <- readFASTA("~/Desktop/protseq.fasta", strip.descs=TRUE)
alm <- pairwiseAlignment(seqs[[1]]$seq, seqs[[2]]$seq, substitutionMatrix=BLOSUM100, gapOpening=0, gapExtension=-5)
The result of this is (removed some of the alignment to save space):
> alm
Global PairwiseAlignedFixedSubject (1 of 1)
pattern: [1] MYRALRLLARSRPLVRA-PAAALAS....
subject: [1] M-R-------SRP---AGPALLLLL....
score: -91
To only extract the score for each alignment:
> score(alm)
[1] -91
Given this you can easily now do all pairwise alignments with some very simple looping logic. To get a better hang of pairwise alignment using bioconductor I suggest you read this.
An alternative approach would be to do a multiple sequence alignment instead of pairwise. You could use bio3d and from there the seqaln function to align all sequences in your fasta file.
回答2:
6 years later, but:
The protr package just came out, which has a parallelized pairwise similarity scoring function, parGOsim(). It can take lists of protein sequences, so a loop wouldn't be necessary to write.
来源：https://stackoverflow.com/questions/6529675/how-to-get-pair-wise-sequence-similarity-score-for-1000-proteins