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Asked: 2026-05-23T12:31:24+00:00

It is a question build upon the previous question (http://stackoverflow.com/questions/6538448/r-how-to-write-a-loop-to-get-a-matrix). It is different from

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It is a question build upon the previous question (http://stackoverflow.com/questions/6538448/r-how-to-write-a-loop-to-get-a-matrix).

It is different from the previous one, as more details is provided, and libraries and example file is provided according to comments from DWin. So, I submitted it as a new question. Could you mind to teach me how to modify this code further?

To load the necessary libraries:

source("http://bioconductor.org/biocLite.R")
biocLite()

My protseq.fasta file has the following contents:

>drugbank_target|1 Peptidoglycan synthetase ftsI (DB00303)  
MVKFNSSRKSGKSKKTIRKLTAPETVKQNKPQKVFEKCFMRGRYMLSTVLILLGLCALVARAAYVQSINADTLSNEADKR
SLRKDEVLSVRGSILDRNGQLLSVSVPMSAIVADPKTMLKENSLADKERIAALAEELGMTENDLVKKIEKNSKSGYLYLA
RQVELSKANYIRRLKIKGIILETEHRRFYPRVEEAAHVVGYTDIDGNGIEGIEKSFNSLLVGKDGSRTVRKDKRGNIVAH
ISDEKKYDAQDVTLSIDEKLQSMVYREIKKAVSENNAESGTAVLVDVRTGEVLAMATAPSYNPNNRVGVKSELMRNRAIT
DTFEPGSTVKPFVVLTALQRGVVKRDEIIDTTSFKLSGKEIVDVAPRAQQTLDEILMNSSNRGVSRLALRMPPSALMETY
QNAGLSKPTDLGLIGEQVGILNANRKRWADIERATVAYGYGITATPLQIARAYATLGSFGVYRPLSITKVDPPVIGKRVF
SEKITKDIVGILEKVAIKNKRAMVEGYRVGVKTGTARKIENGHYVNKYVAFTAGIAPISDPRYALVVLINDPKAGEYYGG
AVSAPVFSNIMGYALRANAIPQDAEAAENTTTKSAKRIVYIGEHKNQKVN
>drugbank_target|3 Histidine decarboxylase (DB00114; DB00117)  
MMEPEEYRERGREMVDYICQYLSTVRERRVTPDVQPGYLRAQLPESAPEDPDSWDSIFGDIERIIMPGVVHWQSPHMHAY
YPALTSWPSLLGDMLADAINCLGFTWASSPACTELEMNVMDWLAKMLGLPEHFLHHHPSSQGGGVLQSTVSESTLIALLA
ARKNKILEMKTSEPDADESCLNARLVAYASDQAHSSVEKAGLISLVKMKFLPVDDNFSLRGEALQKAIEEDKQRGLVPVF
VCATLGTTGVCAFDCLSELGPICAREGLWLHIDAAYAGTAFLCPEFRGFLKGIEYADSFTFNPSKWMMVHFDCTGFWVKD
KYKLQQTFSVNPIYLRHANSGVATDFMHWQIPLSRRFRSVKLWFVIRSFGVKNLQAHVRHGTEMAKYFESLVRNDPSFEI
PAKRHLGLVVFRLKGPNCLTENVLKEIAKAGRLFLIPATIQDKLIIRFTVTSQFTTRDDILRDWNLIRDAATLILSQHCT
SQPSPRVGNLISQIRGARAWACGTSLQSVSGAGDDPVQARKIIKQPQRVGAGPMKRENGLHLETLLDPVDDCFSEEAPDA
TKHKLSSFLFSYLSVQTKKKTVRSLSCNSVPVSAQKPLPTEASVKNGGSSRVRIFSRFPEDMMMLKKSAFKKLIKFYSVP
SFPECSSQCGLQLPCCPLQAMV
>drugbank_target|5 Glutaminase liver isoform, mitochondrial (DB00130; DB00142)  
MRSMKALQKALSRAGSHCGRGGWGHPSRSPLLGGGVRHHLSEAAAQGRETPHSHQPQHQDHDSSESGMLSRLGDLLFYTI
AEGQERTPIHKFTTALKATGLQTSDPRLRDCMSEMHRVVQESSSGGLLDRDLFRKCVSSSIVLLTQAFRKKFVIPDFEEF
TGHVDRIFEDVKELTGGKVAAYIPQLAKSNPDLWGVSLCTVDGQRHSVGHTKIPFCLQSCVKPLTYAISISTLGTDYVHK
FVGKEPSGLRYNKLSLDEEGIPHNPMVNAGAIVVSSLIKMDCNKAEKFDFVLQYLNKMAGNEYMGFSNATFQSEKETGDR
NYAIGYYHEEKKCFPKGVDMMAALDLYFQLCSVEVTCESGSVMAATLANGGICPITGESVLSAEAVRNTLSLMHSCGMYD
FSGQFAFHVGLPAKSAVSGAILLVVPNVMGMMCLSPPLDKLGNSHRGTSFCQKLVSLFNFHNYDNLRHCARKLDPRREGA
EIRNKTVVNLLFAAYSGDVSALRRFALSAMDMEQKDYDSRTALHVAAAEGHIEVVKFLIEACKVNPFAKDRWGNIPLDDA
VQFNHLEVVKLLQDYQDSYTLSETQAEAAAEALSKENLESMV
>drugbank_target|6 Coagulation factor XIII A chain (DB00130; DB01839; DB02340)  
SETSRTAFGGRRAVPPNNSNAAEDDLPTVELQGVVPRGVNLQEFLNVTSVHLFKERWDTNKVDHHTDKYENNKLIVRRGQ
SFYVQIDFSRPYDPRRDLFRVEYVIGRYPQENKGTYIPVPIVSELQSGKWGAKIVMREDRSVRLSIQSSPKCIVGKFRMY
VAVWTPYGVLRTSRNPETDTYILFNPWCEDDAVYLDNEKEREEYVLNDIGVIFYGEVNDIKTRSWSYGQFEDGILDTCLY
VMDRAQMDLSGRGNPIKVSRVGSAMVNAKDDEGVLVGSWDNIYAYGVPPSAWTGSVDILLEYRSSENPVRYGQCWVFAGV
FNTFLRCLGIPARIVTNYFSAHDNDANLQMDIFLEEDGNVNSKLTKDSVWNYHCWNEAWMTRPDLPVGFGGWQAVDSTPQ
ENSDGMYRCGPASVQAIKHGHVCFQFDAPFVFAEVNSDLIYITAKKDGTHVVENVDATHIGKLIVTKQIGGDGMMDITDT
YKFQEGQEEERLALETALMYGAKKPLNTEGVMKSRSNVDMDFEVENAVLGKDFKLSITFRNNSHNRYTITAYLSANITFY
TGVPKAEFKKETFDVTLEPLSFKKEAVLIQAGEYMGQLLEQASLHFFVTARINETRDVLAKQKSTVLTIPEIIIKVRGTQ
VVGSDMTVTVQFTNPLKETLRNVWVHLDGPGVTRPMKKMFREIRPNSTVQWEEVCRPWVSGHRKLIASMSSDSLRHVYGE
LDVQIQRRPSM

To load the data to R for the analysis, I have done:

require("Biostrings")
data(BLOSUM100)
seqs <- readFASTA("./protseq.fasta", strip.descs=TRUE)

To get the the pairwise numbers, as there are a total of 4 sequences, I have done:

number <-c(1:4); dat <- expand.grid(number,number, stringsAsFactors=FALSE)
datr <- dat[dat[,1] > dat[,2] , ]

In order to calculate the score one by one, I can do this:

 score(pairwiseAlignment(seqs[[x]]$seq, seqs[[y]]$seq, substitutionMatrix=BLOSUM100, gapOpening=0, gapExtension=-5))

However, I have problem to add a new column as “score” to include all the score for each pairs of the proteins. I tried to do this, but did not work.

datr$score <- lapply(datr, 1, function(i) { x <- datr[i,1]; y<- datr[i,2]; score(pairwiseAlignment(seqs[[x]]$seq, seqs[[y]]$seq, substitutionMatrix=BLOSUM100, gapOpening=0, gapExtension=-5))})

Could you mind to comments how to further improve it? Thanks DWin and diliop for wonderful solutions to my previous question.

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1 Answer

  1. Editorial Team

    Try:

    datr$score <- sapply(1:nrow(datr), function(i) {
    x <- datr[i,1]
    y <- datr[i,2]
    score(pairwiseAlignment(seqs[[x]]$seq, seqs[[y]]$seq, substitutionMatrix=BLOSUM100,gapOpening=0, gapExtension=-5))
})

    To be able to reference your sequences better using their names, you might want to tidy up datr by doing the following:

    colnames(datr) <- c("seq1id", "seq2id", "score")
datr$seq1name <- sapply(datr$seq1id, function(i) seqs[[i]]$desc)
datr$seq2name <- sapply(datr$seq2id, function(i) seqs[[i]]$desc)

    Or if you just want to extract the accession IDs i.e. the contents of your parentheses, you could use stringr as such:

    library(stringr)
datr$seq1name <- sapply(datr$seq2id, function(i) str_extract(seqs[[i]]$desc, "DB[0-9\\ ;DB]+"))

    Hope this helps!

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