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Question: Align two protein sequences using BLAST
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gravatar for Alla Bulashevska
7.9 years ago by
Alla Bulashevska60 wrote:
Dear Bioconductor users, I would like to align two protein sequences using BLAST (bl2seq). The question is whether this programm have been implemented in R. Thank you for your help, Alla.
ADD COMMENTlink modified 7.9 years ago by Patrick Aboyoun1.6k • written 7.9 years ago by Alla Bulashevska60
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gravatar for Patrick Aboyoun
7.9 years ago by
Patrick Aboyoun1.6k
United States
Patrick Aboyoun1.6k wrote:
Alla, The pairwiseAlignment in the Biostrings package can align (in a local, global, overlap, global-local, local-global fashion) two protein sequences and there are a number of predefined PAM and BLOSUM substitution matrices you can use when constructing the alignment. For more information see library(Biostrings) help(substitution.matrices) help(pairwiseAlignment) Here is an example: > aa1 <- AAString("HXBLVYMGCHFDCXVBEHIKQZ") > aa2 <- AAString("QRNYMYCFQCISGNEYKQN") > pairwiseAlignment(aa1, aa2, substitutionMatrix = "BLOSUM62", gapOpening = -3, gapExtension = -1) Global PairwiseAlignedFixedSubject (1 of 1) pattern: [1] HXBLVYMGCHFDCXV--BEHIKQZ subject: [1] QRN--YMYC-FQC-ISGNEY-KQN score: 38 > sessionInfo() R version 2.11.0 Under development (unstable) (2010-01-02 r50884) i386-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Biostrings_2.15.11 IRanges_1.5.23 loaded via a namespace (and not attached): [1] Biobase_2.7.3 tcltk_2.11.0 tools_2.11.0 Cheers, Patrick Alla Bulashevska wrote: > Dear Bioconductor users, > I would like to align two protein sequences using BLAST > (bl2seq). The question is whether this programm have been > implemented in R. > Thank you for your help, > Alla. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 7.9 years ago by Patrick Aboyoun1.6k
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