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String objects representing biological sequences, and matching algorithms

Bioconductor version: 2.14

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>

Citation (from within R, enter citation("Biostrings")):


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PDF R Script A short presentation of the basic classes defined in Biostrings 2
PDF R Script Biostrings Quick Overview
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
Version 2.32.1
In Bioconductor since BioC 1.6 (R-2.1) or earlier
License Artistic-2.0
Depends R (>= 2.8.0), methods, BiocGenerics(>= 0.5.4), IRanges(>= 1.21.35), XVector(>= 0.3.6)
Imports graphics, methods, stats, utils, BiocGenerics, IRanges, XVector, zlibbioc
Suggests BSgenome(>= 1.13.14), BSgenome.Celegans.UCSC.ce2(>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures(>= 1.3.14), hgu95av2cdf, affy(>= 1.41.3), affydata(>= 1.11.5), RUnit
System Requirements
Depends On Me altcdfenvs, Basic4Cseq, BRAIN, BSgenome, ChIPpeakAnno, ChIPsim, cleaver, CRISPRseek, DASiR, DECIPHER, deepSNV, FDb.FANTOM4.promoters.hg19, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, GeneRegionScan, genomes, GenomicAlignments, GOTHiC, harbChIP, iPAC, JASPAR2014, methVisual, minfi, MotifDb, motifRG, oligo, oneChannelGUI,,,,, pd.nugo.hs1a520180, pd.nugo.mm1a520177,,, PWMEnrich, qrqc, R453Plus1Toolbox, REDseq, rGADEM, Roleswitch, Rsamtools, rSFFreader, RSVSim, sangerseqR, SCAN.UPC, scsR, seqbias, ShortRead, spliceSites, triplex, waveTiling
Imports Me AffyCompatible, AllelicImbalance, ArrayExpressHTS, BCRANK, BEAT, BioSeqClass, biovizBase, BSgenome, charm, ChIPseqR, ChIPsim, CNEr, cobindR, customProDB, dagLogo, easyRNASeq, ensemblVEP, gcrma, GeneRegionScan, GenomicAlignments, GenomicFeatures, ggbio, GGtools, girafe, gmapR, Gviz, gwascat, h5vc, HiTC, HTSeqGenie, KEGGREST, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ESP6500SI.V2.SSA137.dbSNP138, MafDb.ESP6500SI.V2.SSA137.dbSNP138, MEDIPS, MEDME, methVisual, microRNA, motifRG, MotIV, 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.atdschip.tiling, 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.hg18.60mer.expr,,,, pd.hu6800,,,, pd.maize, pd.mapping250k.nsp, pd.mapping250k.sty, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.medicago,,,,,,, pd.mirna.1.0, pd.mirna.2.0, pd.mirna.3.0, pd.mirna.3.1, 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, phyloseq, qrqc, QuasR, Rcpi, REDseq, Repitools, rGADEM, Rolexa, rSFFreader, rtracklayer, SeqArray, SomaticSignatures, synapter, TFBSTools, VariantAnnotation, VariantFiltering, VariantTools
Suggests Me annotate, BeadArrayUseCases, CSAR, exomeCopy, GenomicRanges, genoset, methylumi, microRNA, MiRaGE, pcaGoPromoter, procoil, rpx, rTRM, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119, SNPlocs.Hsapiens.dbSNP.20120608, XVector

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Package Source Biostrings_2.32.1.tar.gz
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