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.

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 >