String objects representing biological sequences, and matching algorithms

Bioconductor version: 2.10

Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

Author: H. Pages, P. Aboyoun, R. Gentleman, and S. DebRoy

Maintainer: H. Pages <hpages at>

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PDF R Script A short presentation of the basic classes defined in Biostrings 2
PDF R Script Handling probe sequence information
PDF R Script Multiple Alignments
PDF R Script Pairwise Sequence Alignments
PDF   Reference Manual
Text   NEWS


biocViews DataImport, DataRepresentation, Genetics, Infrastructure, SequenceMatching, Sequencing, Software
Depends R (>= 2.8.0), methods, BiocGenerics(>= 0.1.2), IRanges(>= 1.13.6)
Imports graphics, methods, stats, utils, BiocGenerics, IRanges
Suggests BSgenome(>= 1.13.14), BSgenome.Celegans.UCSC.ce2(>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.3.11), drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures(>= 1.3.14), hgu95av2cdf, affy, affydata(>= 1.11.5), RUnit
System Requirements
License Artistic-2.0
Depends On Me altcdfenvs, BRAIN, BSgenome, ChIPpeakAnno, ChIPsim, DECIPHER, deepSNV, easyRNASeq, GeneRegionScan, harbChIP, oneChannelGUI,, qrqc, R453Plus1Toolbox, REDseq, rGADEM, Rsamtools, seqbias, ShortRead
Imports Me AffyCompatible, ArrayExpressHTS, BCRANK, BioSeqClass, biovizBase, charm, ChIPpeakAnno, ChIPseqR, ChIPsim, DECIPHER, gcrma, GeneRegionScan, GenomicFeatures, genoset, girafe, gwascat, HiTC, MEDIPS, MEDME, methVisual, microRNA, motifRG, oligo, oligoClasses, OTUbase, pd.081229.hg18.promoter.medip.hx1, pd.2006.07.18.hg18.refseq.promoter, pd.2006.07.18.mm8.refseq.promoter, pd.2006.10.31.rn34.refseq.promoter,,, pd.ath1.121501, pd.barley1,, pd.bovine, pd.bsubtilis,, pd.canine, pd.canine.2, pd.celegans, pd.charm.hg18.example, pd.chicken, pd.citrus, pd.cotton,, pd.cytogenetics.array, pd.drosgenome1, pd.drosophila.2, pd.e.coli.2, pd.ecoli, pd.ecoli.asv2,,,,,, pd.genomewidesnp.5, pd.genomewidesnp.6, pd.hc.g110, pd.hg.focus,, pd.hg.u133a, pd.hg.u133a.2, pd.hg.u133a.tag, pd.hg.u133b, pd.hg.u219, pd.hg.u95a, pd.hg.u95av2, pd.hg.u95b, pd.hg.u95c, pd.hg.u95d, pd.hg.u95e,,,, pd.hu6800,,,, pd.maize, pd.mapping250k.nsp, pd.mapping250k.sty, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.medicago,,,,,,, pd.mirna.1.0, pd.moe430a, pd.moe430b,,,, pd.mouse430.2, pd.mouse430a.2, pd.mu11ksuba, pd.mu11ksubb,,, pd.pae.g1a, pd.plasmodium.anopheles, pd.poplar, pd.porcine,,, pd.rae230a, pd.rae230b,,,, pd.rat230.2, pd.rg.u34a, pd.rg.u34b, pd.rg.u34c,, pd.rhesus, pd.rice, pd.rn.u34, pd.s.aureus, pd.soybean,, pd.sugar.cane, pd.tomato, pd.u133.x3p, pd.vitis.vinifera, pd.wheat, pd.x.laevis.2, pd.x.tropicalis, pd.xenopus.laevis, pd.yeast.2, pd.yg.s98,, pd.zebrafish, pdInfoBuilder, qrqc, R453Plus1Toolbox, REDseq, rGADEM, Rolexa, Rsamtools, rtracklayer, ShortRead, VariantAnnotation
Suggests Me annotate, BeadArrayUseCases, CSAR, exomeCopy, GenomicFeatures, microRNA, minfi, pcaGoPromoter, procoil, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119
Version 2.24.1
Since Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source Biostrings_2.24.1.tar.gz
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MacOS 10.5 (Leopard) binary Biostrings_2.24.1.tgz
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