[BioC] obtaining a complete global alignment via pairwiseAlignment
Robert K.Bradley [guest]
guest at bioconductor.org
Sat Jun 15 04:57:30 CEST 2013
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: [3] GG
subject: [1] 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:
[1] C
attached base packages:
[1] parallel grid grDevices utils datasets stats graphics methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.28.0 org.Hs.eg.db_2.9.0 beanplot_1.1
[5] IlluminaHumanMethylation450kmanifest_0.4.0 goseq_1.12.0 geneLenDataBase_0.99.11 BiasedUrn_1.05
[9] GO.db_2.9.0 RSQLite_0.11.4 DBI_0.2-7 fastcluster_1.1.11
[13] minfi_1.6.0 reshape_0.8.4 plyr_1.8 lattice_0.20-15
[17] FDb.InfiniumMethylation.hg19_1.0.1 rtracklayer_1.20.2 Biostrings_2.28.0 GenomicFeatures_1.12.2
[21] AnnotationDbi_1.22.6 Biobase_2.20.0 GenomicRanges_1.12.4 IRanges_1.18.1
[25] VennDiagram_1.6.0 RColorBrewer_1.0-5 BiocGenerics_0.6.0 gplots_2.11.0.1
[29] MASS_7.3-26 KernSmooth_2.23-10 caTools_1.14 gdata_2.12.0.2
[33] gtools_2.7.1
loaded via a namespace (and not attached):
[1] 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
[9] 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
[17] siggenes_1.34.0 splines_3.0.1 stats4_3.0.1 survival_2.37-4 tools_3.0.1 zlibbioc_1.6.0
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