Biostrings: String objects representing biological sequences, and matching algorithms

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

Author
H. Pagès, P. Aboyoun, R. Gentleman, and S. DebRoy
Date of publication
None
Maintainer
H. Pagès <hpages@fredhutch.org>
License
Artistic-2.0
Version
2.42.1

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