Question: obtaining a complete global alignment via pairwiseAlignment
6.5 years ago by
Guest User • 12k
Guest User • 12k wrote:
Hello, I'm interested in using the pairwiseAlignment function in Biostrings to perform simple alignments of short sequences. I noticed that even the global alignment mode returns an alignment with gapped ends trimmed off. For example: > s1 = DNAString ("AAGGAA") > s2 = DNAString ("GG") > pairwiseAlignment (s1, s2, type = "global") Global PairwiseAlignmentsSingleSubject (1 of 1) pattern:  GG subject:  GG score: -32.03649 Is it possible to obtain the complete alignment including the (possibly) gapped ends? In this case, that would be: --GG-- AAGGAA For my purposes, having the complete gapped alignment is important. My question seems related to a previous post: https://stat.ethz.ch/pipermail/bioconductor/2012-February/043577.html Thank you in advance. Best wishes, Rob -- Robert K. Bradley, Assistant Member Fred Hutchinson Cancer Research Center http://labs.fhcrc.org/bradleyr/ -- output of sessionInfo(): > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale:  C attached base packages:  parallel grid grDevices utils datasets stats graphics methods base other attached packages:  BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.28.0 org.Hs.eg.db_2.9.0 beanplot_1.1  IlluminaHumanMethylation450kmanifest_0.4.0 goseq_1.12.0 geneLenDataBase_0.99.11 BiasedUrn_1.05  GO.db_2.9.0 RSQLite_0.11.4 DBI_0.2-7 fastcluster_1.1.11  minfi_1.6.0 reshape_0.8.4 plyr_1.8 lattice_0.20-15  FDb.InfiniumMethylation.hg19_1.0.1 rtracklayer_1.20.2 Biostrings_2.28.0 GenomicFeatures_1.12.2  AnnotationDbi_1.22.6 Biobase_2.20.0 GenomicRanges_1.12.4 IRanges_1.18.1  VennDiagram_1.6.0 RColorBrewer_1.0-5 BiocGenerics_0.6.0 gplots_22.214.171.124  MASS_7.3-26 KernSmooth_2.23-10 caTools_1.14 gdata_126.96.36.199  gtools_2.7.1 loaded via a namespace (and not attached):  Matrix_1.0-12 R.methodsS3_1.4.2 RCurl_1.95-4.1 Rsamtools_1.12.3 XML_3.95-0.2 biomaRt_2.16.0 bitops_1.0-5 illuminaio_0.2.0  limma_3.16.5 matrixStats_0.8.1 mclust_4.1 mgcv_1.7-24 multtest_2.16.0 nlme_3.1-109 nor1mix_1.1-4 preprocessCore_1.22.0  siggenes_1.34.0 splines_3.0.1 stats4_3.0.1 survival_2.37-4 tools_3.0.1 zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENT • link •