Biostrings: String objects representing biological sequences, and matching algorithms

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

AuthorH. Pagès, P. Aboyoun, R. Gentleman, and S. DebRoy
Date of publicationNone
MaintainerH. Pagès <hpages@fredhutch.org>
LicenseArtistic-2.0
Version2.42.1

View on Bioconductor

Man pages

AAString-class: AAString objects

AlignedXStringSet-class: AlignedXStringSet and QualityAlignedXStringSet objects

align-utils: Utility functions related to sequence alignment

AMINO_ACID_CODE: The Single-Letter Amino Acid Code

Biostrings-internals: Biostrings internals

BOC_SubjectString-class: BOC\_SubjectString and BOC2\_SubjectString objects (DEFUNCT!)

chartr: Translating letters of a sequence

detail: Show (display) detailed object content

dinucleotideFrequencyTest: Pearson's chi-squared Test and G-tests for String Position...

DNAString-class: DNAString objects

findPalindromes: Searching a sequence for palindromes

GENETIC_CODE: The Standard Genetic Code and its known variants

getSeq: getSeq

gregexpr2: A replacement for R standard gregexpr function

HNF4alpha: Known HNF4alpha binding sequences

InDel-class: InDel objects

injectHardMask: Injecting a hard mask in a sequence

IUPAC_CODE_MAP: The IUPAC Extended Genetic Alphabet

letter: Subsetting a string

letterFrequency: Calculate the frequency of letters in a biological sequence,...

longestConsecutive: Obtain the length of the longest substring containing only...

lowlevel-matching: Low-level matching functions

MaskedXString-class: MaskedXString objects

maskMotif: Masking by content (or by position)

matchLRPatterns: Find paired matches in a sequence

matchPattern: String searching functions

matchPDict-exact: Matching a dictionary of patterns against a reference

matchPDict-inexact: Inexact matching with matchPDict()/countPDict()/whichPDict()

matchProbePair: Find "theoretical amplicons" mapped to a probe pair

matchprobes: A function to match a query sequence to the sequences of a...

matchPWM: PWM creating, matching, and related utilities

match-utils: Utility functions operating on the matches returned by a...

MIndex-class: MIndex objects

misc: Some miscellaneous stuff

MultipleAlignment-class: MultipleAlignment objects

needwunsQS: (Deprecated) Needleman-Wunsch Global Alignment

nucleotideFrequency: Calculate the frequency of oligonucleotides in a DNA or RNA...

padAndClip: Pad and clip strings

pairwiseAlignment: Optimal Pairwise Alignment

PairwiseAlignments-class: PairwiseAlignments, PairwiseAlignmentsSingleSubject, and...

PairwiseAlignments-io: Write a PairwiseAlignments object to a file

PDict-class: PDict objects

phiX174Phage: Versions of bacteriophage phiX174 complete genome and sample...

pid: Percent Sequence Identity

pmatchPattern: Longest Common Prefix/Suffix/Substring searching functions

QualityScaledXStringSet-class: QualityScaledBStringSet, QualityScaledDNAStringSet,...

replaceAt: Extract/replace arbitrary substrings from/in a string or set...

replaceLetterAt: Replacing letters in a sequence (or set of sequences) at some...

reverseComplement: Sequence reversing and complementing

RNAString-class: RNAString objects

stringDist: String Distance/Alignment Score Matrix

substitution_matrices: Scoring matrices

toComplex: Turning a DNA sequence into a vector of complex numbers

translate: Translating DNA/RNA sequences

trimLRPatterns: Trim Flanking Patterns from Sequences

xscat: Concatenate sequences contained in XString, XStringSet and/or...

XString-class: BString objects

XStringPartialMatches-class: XStringPartialMatches objects

XStringQuality-class: PhredQuality, SolexaQuality and IlluminaQuality objects

XStringSet-class: XStringSet objects

XStringSet-comparison: Comparing and ordering the elements in one or more XStringSet...

XStringSet-io: Read/write an XStringSet object from/to a file

XStringSetList-class: XStringSetList objects

XStringViews-class: The XStringViews class

yeastSEQCHR1: An annotation data file for CHR1 in the yeastSEQ package

Files in this package

Biostrings/.BBSoptions
Biostrings/CHANGES
Biostrings/DESCRIPTION
Biostrings/NAMESPACE
Biostrings/NEWS
Biostrings/R
Biostrings/R/00datacache.R Biostrings/R/AMINO_ACID_CODE.R Biostrings/R/AlignedXStringSet-class.R Biostrings/R/GENETIC_CODE.R Biostrings/R/IUPAC_CODE_MAP.R Biostrings/R/InDel-class.R Biostrings/R/MIndex-class.R Biostrings/R/MaskedXString-class.R Biostrings/R/MultipleAlignment.R Biostrings/R/PDict-class.R Biostrings/R/PairwiseAlignments-class.R Biostrings/R/PairwiseAlignments-io.R Biostrings/R/PairwiseAlignmentsSingleSubject-class.R Biostrings/R/QualityScaledXStringSet.R Biostrings/R/SparseList-class.R Biostrings/R/XString-class.R Biostrings/R/XStringCodec-class.R Biostrings/R/XStringPartialMatches-class.R Biostrings/R/XStringQuality-class.R Biostrings/R/XStringSet-class.R Biostrings/R/XStringSet-comparison.R Biostrings/R/XStringSet-io.R Biostrings/R/XStringSetList-class.R Biostrings/R/XStringViews-class.R Biostrings/R/align-utils.R Biostrings/R/chartr.R Biostrings/R/dinucleotideFrequencyTest.R Biostrings/R/findPalindromes.R Biostrings/R/getSeq.R Biostrings/R/injectHardMask.R Biostrings/R/letter.R Biostrings/R/letterFrequency.R Biostrings/R/lowlevel-matching.R Biostrings/R/maskMotif.R Biostrings/R/match-utils.R Biostrings/R/matchLRPatterns.R Biostrings/R/matchPDict.R Biostrings/R/matchPWM.R Biostrings/R/matchPattern.BOC.R Biostrings/R/matchPattern.BOC2.R Biostrings/R/matchPattern.R Biostrings/R/matchProbePair.R Biostrings/R/matchprobes.R Biostrings/R/misc.R Biostrings/R/needwunsQS.R Biostrings/R/padAndClip.R Biostrings/R/pairwiseAlignment.R Biostrings/R/pmatchPattern.R Biostrings/R/replaceAt.R Biostrings/R/replaceLetterAt.R Biostrings/R/reverseComplement.R Biostrings/R/seqtype.R Biostrings/R/stringDist.R Biostrings/R/toComplex.R Biostrings/R/translate.R Biostrings/R/trimLRPatterns.R Biostrings/R/unstrsplit-methods.R Biostrings/R/utils.R Biostrings/R/xscat.R Biostrings/R/zzz.R
Biostrings/TODO
Biostrings/build
Biostrings/build/vignette.rds
Biostrings/data
Biostrings/data/BLOSUM100.rda
Biostrings/data/BLOSUM45.rda
Biostrings/data/BLOSUM50.rda
Biostrings/data/BLOSUM62.rda
Biostrings/data/BLOSUM80.rda
Biostrings/data/HNF4alpha.rda
Biostrings/data/PAM120.rda
Biostrings/data/PAM250.rda
Biostrings/data/PAM30.rda
Biostrings/data/PAM40.rda
Biostrings/data/PAM70.rda
Biostrings/data/phiX174Phage.rda
Biostrings/data/srPhiX174.rda
Biostrings/data/yeastSEQCHR1.rda
Biostrings/devtools
Biostrings/devtools/rgrep-tip.txt
Biostrings/inst
Biostrings/inst/doc
Biostrings/inst/doc/Biostrings2Classes.R
Biostrings/inst/doc/Biostrings2Classes.Rnw
Biostrings/inst/doc/Biostrings2Classes.pdf
Biostrings/inst/doc/BiostringsQuickOverview.Rnw
Biostrings/inst/doc/BiostringsQuickOverview.pdf
Biostrings/inst/doc/MultipleAlignments.R
Biostrings/inst/doc/MultipleAlignments.Rnw
Biostrings/inst/doc/MultipleAlignments.pdf
Biostrings/inst/doc/PairwiseAlignments.R
Biostrings/inst/doc/PairwiseAlignments.Rnw
Biostrings/inst/doc/PairwiseAlignments.pdf
Biostrings/inst/doc/matchprobes.R
Biostrings/inst/doc/matchprobes.Rnw
Biostrings/inst/doc/matchprobes.pdf
Biostrings/inst/extdata
Biostrings/inst/extdata/Phylip.txt
Biostrings/inst/extdata/README
Biostrings/inst/extdata/Sc.fa
Biostrings/inst/extdata/Sp.fa
Biostrings/inst/extdata/dm3_upstream2000.fa.gz
Biostrings/inst/extdata/fastaEx.fa
Biostrings/inst/extdata/hg18chr8_gap.txt
Biostrings/inst/extdata/hg18chrY_gap.txt
Biostrings/inst/extdata/msx2_mRNA.aln
Biostrings/inst/extdata/s_1_sequence.txt
Biostrings/inst/extdata/someORF.fa
Biostrings/inst/extdata/someORF.fa.gz
Biostrings/inst/include
Biostrings/inst/include/Biostrings_defines.h
Biostrings/inst/include/Biostrings_interface.h
Biostrings/inst/include/_Biostrings_stubs.c
Biostrings/inst/unitTests
Biostrings/inst/unitTests/test_MultipleAlignment.R
Biostrings/inst/unitTests/test_XString.R
Biostrings/inst/unitTests/test_XStringSet.R
Biostrings/inst/unitTests/test_XStringSetList.R
Biostrings/inst/unitTests/test_findPalindromes.R
Biostrings/inst/unitTests/test_matchDNAPattern.R.FIXME
Biostrings/inst/unitTests/test_matchPDict.R
Biostrings/inst/unitTests/test_pairwiseAlignment.R
Biostrings/inst/unitTests/test_twoWayAlphabetFrequency.R
Biostrings/man
Biostrings/man/AAString-class.Rd Biostrings/man/AMINO_ACID_CODE.Rd Biostrings/man/AlignedXStringSet-class.Rd Biostrings/man/BOC_SubjectString-class.Rd Biostrings/man/Biostrings-internals.Rd Biostrings/man/DNAString-class.Rd Biostrings/man/GENETIC_CODE.Rd Biostrings/man/HNF4alpha.Rd Biostrings/man/IUPAC_CODE_MAP.Rd Biostrings/man/InDel-class.Rd Biostrings/man/MIndex-class.Rd Biostrings/man/MaskedXString-class.Rd Biostrings/man/MultipleAlignment-class.Rd Biostrings/man/PDict-class.Rd Biostrings/man/PairwiseAlignments-class.Rd Biostrings/man/PairwiseAlignments-io.Rd Biostrings/man/QualityScaledXStringSet-class.Rd Biostrings/man/RNAString-class.Rd Biostrings/man/XString-class.Rd Biostrings/man/XStringPartialMatches-class.Rd Biostrings/man/XStringQuality-class.Rd Biostrings/man/XStringSet-class.Rd Biostrings/man/XStringSet-comparison.Rd Biostrings/man/XStringSet-io.Rd Biostrings/man/XStringSetList-class.Rd Biostrings/man/XStringViews-class.Rd Biostrings/man/align-utils.Rd Biostrings/man/chartr.Rd Biostrings/man/detail.Rd Biostrings/man/dinucleotideFrequencyTest.Rd Biostrings/man/findPalindromes.Rd Biostrings/man/getSeq.Rd Biostrings/man/gregexpr2.Rd Biostrings/man/injectHardMask.Rd Biostrings/man/letter.Rd Biostrings/man/letterFrequency.Rd Biostrings/man/longestConsecutive.Rd Biostrings/man/lowlevel-matching.Rd Biostrings/man/maskMotif.Rd Biostrings/man/match-utils.Rd Biostrings/man/matchLRPatterns.Rd Biostrings/man/matchPDict-exact.Rd Biostrings/man/matchPDict-inexact.Rd Biostrings/man/matchPWM.Rd Biostrings/man/matchPattern.Rd Biostrings/man/matchProbePair.Rd Biostrings/man/matchprobes.Rd Biostrings/man/misc.Rd Biostrings/man/needwunsQS.Rd Biostrings/man/nucleotideFrequency.Rd Biostrings/man/padAndClip.Rd Biostrings/man/pairwiseAlignment.Rd Biostrings/man/phiX174Phage.Rd Biostrings/man/pid.Rd Biostrings/man/pmatchPattern.Rd Biostrings/man/replaceAt.Rd Biostrings/man/replaceLetterAt.Rd Biostrings/man/reverseComplement.Rd Biostrings/man/stringDist.Rd Biostrings/man/substitution_matrices.Rd Biostrings/man/toComplex.Rd Biostrings/man/translate.Rd Biostrings/man/trimLRPatterns.Rd Biostrings/man/xscat.Rd Biostrings/man/yeastSEQCHR1.Rd
Biostrings/src
Biostrings/src/BAB_class.c
Biostrings/src/Biostrings.h
Biostrings/src/BitMatrix.c
Biostrings/src/IRanges_stubs.c
Biostrings/src/MIndex_class.c
Biostrings/src/PreprocessedTB_class.c
Biostrings/src/R_init_Biostrings.c
Biostrings/src/RoSeqs_utils.c
Biostrings/src/S4Vectors_stubs.c
Biostrings/src/SparseList_utils.c
Biostrings/src/XStringSetList_class.c
Biostrings/src/XStringSet_class.c
Biostrings/src/XStringSet_io.c
Biostrings/src/XString_class.c
Biostrings/src/XVector_stubs.c
Biostrings/src/align_needwunsQS.c
Biostrings/src/align_pairwiseAlignment.c
Biostrings/src/align_utils.c
Biostrings/src/find_palindromes.c
Biostrings/src/gtestsim.c
Biostrings/src/inject_code.c
Biostrings/src/letter_frequency.c
Biostrings/src/lowlevel_matching.c
Biostrings/src/match_PWM.c
Biostrings/src/match_pattern.c
Biostrings/src/match_pattern_boyermoore.c
Biostrings/src/match_pattern_indels.c
Biostrings/src/match_pattern_shiftor.c
Biostrings/src/match_pdict.c
Biostrings/src/match_pdict_ACtree2.c
Biostrings/src/match_pdict_Twobit.c
Biostrings/src/match_pdict_utils.c
Biostrings/src/match_reporting.c
Biostrings/src/matchprobes.c
Biostrings/src/pmatchPattern.c
Biostrings/src/replaceAt.c
Biostrings/src/replace_letter_at.c
Biostrings/src/strutils.c
Biostrings/src/translate.c
Biostrings/src/unstrsplit_methods.c
Biostrings/src/utils.c
Biostrings/src/xscat.c
Biostrings/tests
Biostrings/tests/run_unitTests.R
Biostrings/vignettes
Biostrings/vignettes/Biostrings2Classes.Rnw
Biostrings/vignettes/BiostringsQuickOverview.Rnw
Biostrings/vignettes/MultipleAlignments.Rnw
Biostrings/vignettes/PairwiseAlignments.Rnw
Biostrings/vignettes/SolexaYi2-benchmark.txt
Biostrings/vignettes/matchprobes.Rnw

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