Biostrings: String objects representing biological sequences, and matching algorithms
Version 2.44.0

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
Bioconductor views Alignment DataImport DataRepresentation Genetics Infrastructure SequenceMatching Sequencing
Date of publicationNone
MaintainerH. Pagès <hpages@fredhutch.org>
LicenseArtistic-2.0
Version2.44.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Biostrings")

Popular man pages

AMINO_ACID_CODE: The Single-Letter Amino Acid Code
IUPAC_CODE_MAP: The IUPAC Extended Genetic Alphabet
maskMotif: Masking by content (or by position)
matchPattern: String searching functions
matchPWM: PWM creating, matching, and related utilities
stringDist: String Distance/Alignment Score Matrix
translate: Translating DNA/RNA sequences
See all...

All man pages Function index File listing

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
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

Functions

Files

.BBSoptions
CHANGES
DESCRIPTION
NAMESPACE
NEWS
R
R/00datacache.R
R/AMINO_ACID_CODE.R
R/AlignedXStringSet-class.R
R/GENETIC_CODE.R
R/IUPAC_CODE_MAP.R
R/InDel-class.R
R/MIndex-class.R
R/MaskedXString-class.R
R/MultipleAlignment.R
R/PDict-class.R
R/PairwiseAlignments-class.R
R/PairwiseAlignments-io.R
R/PairwiseAlignmentsSingleSubject-class.R
R/QualityScaledXStringSet.R
R/SparseList-class.R
R/XString-class.R
R/XStringCodec-class.R
R/XStringPartialMatches-class.R
R/XStringQuality-class.R
R/XStringSet-class.R
R/XStringSet-comparison.R
R/XStringSet-io.R
R/XStringSetList-class.R
R/XStringViews-class.R
R/align-utils.R
R/chartr.R
R/dinucleotideFrequencyTest.R
R/findPalindromes.R
R/getSeq.R
R/injectHardMask.R
R/letter.R
R/letterFrequency.R
R/lowlevel-matching.R
R/maskMotif.R
R/match-utils.R
R/matchLRPatterns.R
R/matchPDict.R
R/matchPWM.R
R/matchPattern.R
R/matchProbePair.R
R/matchprobes.R
R/misc.R
R/needwunsQS.R
R/padAndClip.R
R/pairwiseAlignment.R
R/pmatchPattern.R
R/replaceAt.R
R/replaceLetterAt.R
R/reverseComplement.R
R/seqtype.R
R/stringDist.R
R/strsplit-methods.R
R/toComplex.R
R/translate.R
R/trimLRPatterns.R
R/utils.R
R/xscat.R
R/zzz.R
TODO
build
build/vignette.rds
data
data/BLOSUM100.rda
data/BLOSUM45.rda
data/BLOSUM50.rda
data/BLOSUM62.rda
data/BLOSUM80.rda
data/HNF4alpha.rda
data/PAM120.rda
data/PAM250.rda
data/PAM30.rda
data/PAM40.rda
data/PAM70.rda
data/phiX174Phage.rda
data/srPhiX174.rda
data/yeastSEQCHR1.rda
devtools
devtools/rgrep-tip.txt
inst
inst/doc
inst/doc/Biostrings2Classes.R
inst/doc/Biostrings2Classes.Rnw
inst/doc/Biostrings2Classes.pdf
inst/doc/BiostringsQuickOverview.Rnw
inst/doc/BiostringsQuickOverview.pdf
inst/doc/MultipleAlignments.R
inst/doc/MultipleAlignments.Rnw
inst/doc/MultipleAlignments.pdf
inst/doc/PairwiseAlignments.R
inst/doc/PairwiseAlignments.Rnw
inst/doc/PairwiseAlignments.pdf
inst/doc/matchprobes.R
inst/doc/matchprobes.Rnw
inst/doc/matchprobes.pdf
inst/extdata
inst/extdata/Phylip.txt
inst/extdata/README
inst/extdata/Sc.fa
inst/extdata/Sp.fa
inst/extdata/dm3_upstream2000.fa.gz
inst/extdata/fastaEx.fa
inst/extdata/hg18chr8_gap.txt
inst/extdata/hg18chrY_gap.txt
inst/extdata/msx2_mRNA.aln
inst/extdata/s_1_sequence.txt
inst/extdata/someORF.fa
inst/extdata/someORF.fa.gz
inst/include
inst/include/Biostrings_defines.h
inst/include/Biostrings_interface.h
inst/include/_Biostrings_stubs.c
inst/unitTests
inst/unitTests/test_MultipleAlignment.R
inst/unitTests/test_XString.R
inst/unitTests/test_XStringSet.R
inst/unitTests/test_XStringSetList.R
inst/unitTests/test_findPalindromes.R
inst/unitTests/test_matchDNAPattern.R.FIXME
inst/unitTests/test_matchPDict.R
inst/unitTests/test_pairwiseAlignment.R
inst/unitTests/test_twoWayAlphabetFrequency.R
man
man/AAString-class.Rd
man/AMINO_ACID_CODE.Rd
man/AlignedXStringSet-class.Rd
man/Biostrings-internals.Rd
man/DNAString-class.Rd
man/GENETIC_CODE.Rd
man/HNF4alpha.Rd
man/IUPAC_CODE_MAP.Rd
man/InDel-class.Rd
man/MIndex-class.Rd
man/MaskedXString-class.Rd
man/MultipleAlignment-class.Rd
man/PDict-class.Rd
man/PairwiseAlignments-class.Rd
man/PairwiseAlignments-io.Rd
man/QualityScaledXStringSet-class.Rd
man/RNAString-class.Rd
man/XString-class.Rd
man/XStringPartialMatches-class.Rd
man/XStringQuality-class.Rd
man/XStringSet-class.Rd
man/XStringSet-comparison.Rd
man/XStringSet-io.Rd
man/XStringSetList-class.Rd
man/XStringViews-class.Rd
man/align-utils.Rd
man/chartr.Rd
man/detail.Rd
man/dinucleotideFrequencyTest.Rd
man/findPalindromes.Rd
man/getSeq.Rd
man/gregexpr2.Rd
man/injectHardMask.Rd
man/letter.Rd
man/letterFrequency.Rd
man/longestConsecutive.Rd
man/lowlevel-matching.Rd
man/maskMotif.Rd
man/match-utils.Rd
man/matchLRPatterns.Rd
man/matchPDict-exact.Rd
man/matchPDict-inexact.Rd
man/matchPWM.Rd
man/matchPattern.Rd
man/matchProbePair.Rd
man/matchprobes.Rd
man/misc.Rd
man/needwunsQS.Rd
man/nucleotideFrequency.Rd
man/padAndClip.Rd
man/pairwiseAlignment.Rd
man/phiX174Phage.Rd
man/pid.Rd
man/pmatchPattern.Rd
man/replaceAt.Rd
man/replaceLetterAt.Rd
man/reverseComplement.Rd
man/stringDist.Rd
man/substitution_matrices.Rd
man/toComplex.Rd
man/translate.Rd
man/trimLRPatterns.Rd
man/xscat.Rd
man/yeastSEQCHR1.Rd
src
src/BAB_class.c
src/Biostrings.h
src/BitMatrix.c
src/IRanges_stubs.c
src/MIndex_class.c
src/PreprocessedTB_class.c
src/R_init_Biostrings.c
src/RoSeqs_utils.c
src/S4Vectors_stubs.c
src/SparseList_utils.c
src/XStringSetList_class.c
src/XStringSet_class.c
src/XStringSet_io.c
src/XString_class.c
src/XVector_stubs.c
src/align_needwunsQS.c
src/align_pairwiseAlignment.c
src/align_utils.c
src/find_palindromes.c
src/gtestsim.c
src/inject_code.c
src/letter_frequency.c
src/lowlevel_matching.c
src/match_PWM.c
src/match_pattern.c
src/match_pattern_boyermoore.c
src/match_pattern_indels.c
src/match_pattern_shiftor.c
src/match_pdict.c
src/match_pdict_ACtree2.c
src/match_pdict_Twobit.c
src/match_pdict_utils.c
src/match_reporting.c
src/matchprobes.c
src/pmatchPattern.c
src/replaceAt.c
src/replace_letter_at.c
src/strutils.c
src/translate.c
src/unstrsplit_methods.c
src/utils.c
src/xscat.c
tests
tests/run_unitTests.R
vignettes
vignettes/Biostrings2Classes.Rnw
vignettes/BiostringsQuickOverview.Rnw
vignettes/MultipleAlignments.Rnw
vignettes/PairwiseAlignments.Rnw
vignettes/SolexaYi2-benchmark.txt
vignettes/matchprobes.Rnw
Biostrings documentation built on May 20, 2017, 10:04 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.