Entry: AAString-class
Aliases: class:AAString AAString-class AA_ALPHABET AAString alphabet,AAString-method
Keywords: methods classes
Description: AAString objects
URL: ../../../library/Biostrings/html/AAString-class.html

Entry: AMINO_ACID_CODE
Aliases: AMINO_ACID_CODE
Keywords: utilities data
Description: The Single-Letter Amino Acid Code
URL: ../../../library/Biostrings/html/AMINO_ACID_CODE.html

Entry: AlignedXStringSet-class
Aliases: class:AlignedXStringSet AlignedXStringSet-class AlignedXStringSet class:QualityAlignedXStringSet QualityAlignedXStringSet-class QualityAlignedXStringSet initialize,AlignedXStringSet-method initialize,QualityAlignedXStringSet-method unaligned unaligned,AlignedXStringSet-method aligned aligned,AlignedXStringSet-method start,AlignedXStringSet-method end,AlignedXStringSet-method width,AlignedXStringSet-method indel indel,AlignedXStringSet-method nindel nindel,AlignedXStringSet-method length,AlignedXStringSet-method nchar,AlignedXStringSet-method alphabet,AlignedXStringSet-method show,AlignedXStringSet-method as.character,AlignedXStringSet-method toString,AlignedXStringSet-method [,AlignedXStringSet,ANY,ANY,ANY-method [,QualityAlignedXStringSet,ANY,ANY,ANY-method [<-,AlignedXStringSet,ANY,ANY,ANY-method rep,AlignedXStringSet-method
Keywords: methods classes
Description: AlignedXStringSet and QualityAlignedXStringSet objects
URL: ../../../library/Biostrings/html/AlignedXStringSet-class.html

Entry: BOC_SubjectString-class
Aliases: class:BOC_SubjectString BOC_SubjectString-class BOC_SubjectString class:BOC2_SubjectString BOC2_SubjectString-class BOC2_SubjectString initialize,BOC_SubjectString-method initialize,BOC2_SubjectString-method matchPattern,BOC_SubjectString-method matchPattern,BOC2_SubjectString-method countPattern,BOC2_SubjectString-method
Keywords: methods classes
Description: BOC\_SubjectString and BOC2\_SubjectString objects
URL: ../../../library/Biostrings/html/BOC_SubjectString-class.html

Entry: Biostrings internals
Aliases: class:Dups Dups-class Dups length,Dups-method duplicated,Dups-method show,Dups-method class:SparseList SparseList-class SparseList length,SparseList-method ls,SparseList-method as.list,SparseList-method [[,SparseList-method class:XStringCodec XStringCodec-class XStringCodec initialize,XStringCodec-method alphabet,XStringCodec-method
Keywords: internal methods classes
Description: Biostrings internals
URL: ../../../library/Biostrings/html/Biostrings-internals.html

Entry: DNAString-class
Aliases: class:DNAString DNAString-class DNA_BASES DNA_ALPHABET DNAString alphabet,DNAString-method
Keywords: methods classes
Description: DNAString objects
URL: ../../../library/Biostrings/html/DNAString-class.html

Entry: GENETIC_CODE
Aliases: GENETIC_CODE RNA_GENETIC_CODE
Keywords: utilities data
Description: The Standard Genetic Code
URL: ../../../library/Biostrings/html/GENETIC_CODE.html

Entry: IUPAC_CODE_MAP
Aliases: IUPAC_CODE_MAP mergeIUPACLetters
Keywords: utilities data
Description: The IUPAC Extended Genetic Alphabet
URL: ../../../library/Biostrings/html/IUPAC_CODE_MAP.html

Entry: InDel-class
Aliases: class:InDel InDel-class InDel insertion insertion,InDel-method deletion deletion,InDel-method
Keywords: methods classes
Description: InDel objects
URL: ../../../library/Biostrings/html/InDel-class.html

Entry: MIndex-class
Aliases: MIndex class:MIndex MIndex-class class:ByPos_MIndex ByPos_MIndex-class length,MIndex-method names,MIndex-method names<-,MIndex-method startIndex endIndex countIndex countIndex,MIndex-method unlist,MIndex-method show,ByPos_MIndex-method [[,ByPos_MIndex-method startIndex,ByPos_MIndex-method endIndex,ByPos_MIndex-method countIndex,ByPos_MIndex-method
Keywords: methods classes
Description: MIndex objects
URL: ../../../library/Biostrings/html/MIndex-class.html

Entry: MaskedXString-class
Aliases: class:MaskedXString MaskedXString-class MaskedXString class:MaskedBString MaskedBString-class MaskedBString class:MaskedDNAString MaskedDNAString-class MaskedDNAString class:MaskedRNAString MaskedRNAString-class MaskedRNAString class:MaskedAAString MaskedAAString-class MaskedAAString unmasked unmasked,MaskedXString-method masks masks,XString-method masks,MaskedXString-method alphabet,MaskedXString-method length,MaskedXString-method maskedwidth,MaskedXString-method maskedratio,MaskedXString-method nchar,MaskedXString-method coerce,BString,MaskedBString-method coerce,DNAString,MaskedDNAString-method coerce,RNAString,MaskedRNAString-method coerce,AAString,MaskedAAString-method coerce,MaskedBString,BString-method coerce,MaskedDNAString,DNAString-method coerce,MaskedRNAString,RNAString-method coerce,MaskedAAString,AAString-method XString,MaskedXString-method coerce,MaskedXString,MaskCollection-method coerce,MaskedXString,NormalIRanges-method coerce,MaskedXString,XStringViews-method reduce,MaskedXString-method gaps,MaskedXString-method subseq,MaskedXString-method as.character,MaskedXString-method toString,MaskedXString-method show,MaskedXString-method masks<- masks<-,MaskedXString,NULL-method masks<-,MaskedXString,MaskCollection-method masks<-,XString,NULL-method masks<-,XString,ANY-method Views,MaskedXString-method
Keywords: methods classes
Description: MaskedXString objects
URL: ../../../library/Biostrings/html/MaskedXString-class.html

Entry: PDict-class
Aliases: class:PreprocessedTB PreprocessedTB-class PreprocessedTB length,PreprocessedTB-method width,PreprocessedTB-method tb tb,PreprocessedTB-method tb.width tb.width,PreprocessedTB-method initialize,PreprocessedTB-method duplicated,PreprocessedTB-method class:Twobit Twobit-class Twobit show,Twobit-method initialize,Twobit-method class:ACtree ACtree-class ACtree show,ACtree-method [,ACtree,ANY,ANY,ANY-method as.matrix,ACtree-method initialize,ACtree-method class:ACtree2 ACtree2-class ACtree2 show,ACtree2-method initialize,ACtree2-method class:PDict3Parts PDict3Parts-class PDict3Parts length,PDict3Parts-method width,PDict3Parts-method head,PDict3Parts-method tb,PDict3Parts-method tb.width,PDict3Parts-method tail,PDict3Parts-method class:PDict PDict-class length,PDict-method width,PDict-method names,PDict-method names<-,PDict-method [[,PDict-method duplicated,PDict-method patternFrequency patternFrequency,PDict-method class:TB_PDict TB_PDict-class TB_PDict head,TB_PDict-method tb,TB_PDict-method tb.width,TB_PDict-method tail,TB_PDict-method show,TB_PDict-method class:MTB_PDict MTB_PDict-class MTB_PDict as.list,MTB_PDict-method show,MTB_PDict-method PDict PDict,character-method PDict,DNAStringSet-method PDict,XStringViews-method PDict,AsIs-method
Keywords: methods classes
Description: PDict objects
URL: ../../../library/Biostrings/html/PDict-class.html

Entry: PairwiseAlignedFixedSubject-class
Aliases: class:PairwiseAlignedFixedSubject PairwiseAlignedFixedSubject-class PairwiseAlignedFixedSubject class:PairwiseAlignedFixedSubjectSummary PairwiseAlignedFixedSubjectSummary-class PairwiseAlignedFixedSubjectSummary initialize,PairwiseAlignedFixedSubject-method pattern,PairwiseAlignedFixedSubject-method subject,PairwiseAlignedFixedSubject-method type type,PairwiseAlignedFixedSubject-method type,PairwiseAlignedFixedSubjectSummary-method score score,PairwiseAlignedFixedSubject-method score,PairwiseAlignedFixedSubjectSummary-method nindel,PairwiseAlignedFixedSubject-method nindel,PairwiseAlignedFixedSubjectSummary-method length,PairwiseAlignedFixedSubject-method length,PairwiseAlignedFixedSubjectSummary-method nchar,PairwiseAlignedFixedSubject-method nchar,PairwiseAlignedFixedSubjectSummary-method alphabet,PairwiseAlignedFixedSubject-method aligned,PairwiseAlignedFixedSubject-method Views,PairwiseAlignedFixedSubject-method show,PairwiseAlignedFixedSubject-method show,PairwiseAlignedFixedSubjectSummary-method summary,PairwiseAlignedFixedSubject-method as.character,PairwiseAlignedFixedSubject-method toString,PairwiseAlignedFixedSubject-method as.matrix,PairwiseAlignedFixedSubject-method [,PairwiseAlignedFixedSubject,ANY,ANY,ANY-method [<-,PairwiseAlignedFixedSubject,ANY,ANY,ANY-method rep,PairwiseAlignedFixedSubject-method
Keywords: methods classes
Description: PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
URL: ../../../library/Biostrings/html/PairwiseAlignedFixedSubject-class.html

Entry: QualityScaledXStringSet-class
Aliases: class:QualityScaledXStringSet QualityScaledXStringSet-class QualityScaledXStringSet class:QualityScaledBStringSet QualityScaledBStringSet-class QualityScaledBStringSet class:QualityScaledDNAStringSet QualityScaledDNAStringSet-class QualityScaledDNAStringSet class:QualityScaledRNAStringSet QualityScaledRNAStringSet-class QualityScaledRNAStringSet class:QualityScaledAAStringSet QualityScaledAAStringSet-class QualityScaledAAStringSet quality quality,QualityScaledXStringSet-method narrow,QualityScaledXStringSet-method append,QualityScaledXStringSet,QualityScaledXStringSet-method show,QualityScaledXStringSet-method [,QualityScaledXStringSet,ANY,ANY,ANY-method
Keywords: methods classes
Description: QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
URL: ../../../library/Biostrings/html/QualityScaledXStringSet-class.html

Entry: RNAString-class
Aliases: class:RNAString RNAString-class RNA_BASES RNA_ALPHABET RNAString alphabet,RNAString-method
Keywords: methods classes
Description: RNAString objects
URL: ../../../library/Biostrings/html/RNAString-class.html

Entry: XString-class
Aliases: class:XString XString-class class:BString BString-class XString XString,character-method XString,AsIs-method XString,XString-method BString alphabet alphabet,BString-method length,XString-method nchar,XString-method as.character,XString-method toString,XString-method show,XString-method [,XString,ANY,ANY,ANY-method ==,XString,XString-method ==,BString,character-method ==,character,BString-method !=,XString,XString-method !=,BString,character-method !=,character,BString-method
Keywords: methods classes
Description: BString objects
URL: ../../../library/Biostrings/html/XString-class.html

Entry: XStringPartialMatches-class
Aliases: class:XStringPartialMatches XStringPartialMatches-class subpatterns subpatterns,XStringPartialMatches-method pattern pattern,XStringPartialMatches-method show,XStringPartialMatches-method [,XStringPartialMatches,ANY,ANY,ANY-method
Keywords: methods classes
Description: XStringPartialMatches objects
URL: ../../../library/Biostrings/html/XStringPartialMatches-class.html

Entry: XStringQuality-class
Aliases: class:XStringQuality XStringQuality-class XStringQuality class:PhredQuality PhredQuality-class PhredQuality class:SolexaQuality SolexaQuality-class SolexaQuality coerce,character,PhredQuality-method coerce,BString,PhredQuality-method coerce,BStringSet,PhredQuality-method coerce,integer,PhredQuality-method coerce,numeric,PhredQuality-method coerce,PhredQuality,integer-method as.integer,PhredQuality-method coerce,PhredQuality,numeric-method as.numeric,PhredQuality-method coerce,character,SolexaQuality-method coerce,BString,SolexaQuality-method coerce,BStringSet,SolexaQuality-method coerce,integer,SolexaQuality-method coerce,numeric,SolexaQuality-method coerce,SolexaQuality,integer-method as.integer,SolexaQuality-method coerce,SolexaQuality,numeric-method as.numeric,SolexaQuality-method
Keywords: methods classes
Description: PhredQuality and SolexaQuality objects
URL: ../../../library/Biostrings/html/XStringQuality-class.html

Entry: XStringSet-class
Aliases: class:XStringSet XStringSet-class XStringSet class:BStringSet BStringSet-class BStringSet class:DNAStringSet DNAStringSet-class DNAStringSet class:RNAStringSet RNAStringSet-class RNAStringSet class:AAStringSet AAStringSet-class AAStringSet length,XStringSet-method width,XStringSet-method names,XStringSet-method names<-,XStringSet-method narrow,XStringSet-method alphabet,XStringSet-method nchar,XStringSet-method coerce,XStringSet,BStringSet-method coerce,XStringSet,DNAStringSet-method coerce,XStringSet,RNAStringSet-method coerce,XStringSet,AAStringSet-method XStringSet,character-method XStringSet,AsIs-method XStringSet,XString-method XStringSet,XStringSet-method XStringSet,XStringViews-method BStringSet DNAStringSet RNAStringSet AAStringSet show,XStringSet-method [,XStringSet,ANY,ANY,ANY-method rep,XStringSet-method [[,XStringSet-method [[<-,XStringSet-method append,XStringSet,XStringSet-method as.character,XStringSet-method toString,XStringSet-method as.matrix,XStringSet-method order order,XStringSet-method sort,XStringSet-method
Keywords: methods classes
Description: BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
URL: ../../../library/Biostrings/html/XStringSet-class.html

Entry: XStringSet-io
Aliases: read.XStringViews read.BStringSet read.DNAStringSet read.RNAStringSet read.AAStringSet write.XStringSet write.XStringViews FASTArecordsToCharacter CharacterToFASTArecords FASTArecordsToXStringViews XStringSetToFASTArecords read.BStringViews write.BStringViews FASTArecordsToBStringViews
Keywords: utilities manip
Description: Read/write an XStringSet or XStringViews object from/to a file
URL: ../../../library/Biostrings/html/XStringSet-io.html

Entry: XStringViews-class
Aliases: class:XStringViews XStringViews-class Views,XString-method Views,character-method alphabet,XStringViews-method nchar,XStringViews-method show,XStringViews-method ==,XStringViews,XStringViews-method ==,XStringViews,XString-method ==,XStringViews,character-method ==,XString,XStringViews-method ==,character,XStringViews-method !=,XStringViews,XStringViews-method !=,XStringViews,XString-method !=,XStringViews,character-method !=,XString,XStringViews-method !=,character,XStringViews-method as.character,XStringViews-method as.matrix,XStringViews-method toString,XStringViews-method
Keywords: methods classes
Description: The XStringViews class
URL: ../../../library/Biostrings/html/XStringViews-class.html

Entry: XStringViews-constructors
Aliases: XStringViews-constructors adjacentViews XStringViews XStringViews,ANY-method XStringViews,XString-method XStringViews,XStringViews-method BStringViews BStringViews,ANY-method BStringViews,file-method BStringViews,XString-method BStringViews,XStringViews-method
Keywords: methods
Description: Basic functions for creating or modifying XStringViews objects
URL: ../../../library/Biostrings/html/XStringViews-constructors.html

Entry: align-utils
Aliases: align-utils mismatch,AlignedXStringSet,missing-method nmatch,PairwiseAlignedFixedSubject,missing-method nmatch,PairwiseAlignedFixedSubjectSummary,missing-method nmismatch,AlignedXStringSet,missing-method nmismatch,PairwiseAlignedFixedSubject,missing-method nmismatch,PairwiseAlignedFixedSubjectSummary,missing-method mismatchTable mismatchTable,AlignedXStringSet-method mismatchTable,QualityAlignedXStringSet-method mismatchTable,PairwiseAlignedFixedSubject-method mismatchSummary mismatchSummary,AlignedXStringSet-method mismatchSummary,QualityAlignedXStringSet-method mismatchSummary,PairwiseAlignedFixedSubject-method mismatchSummary,PairwiseAlignedFixedSubjectSummary-method coverage,AlignedXStringSet-method coverage,PairwiseAlignedFixedSubject-method coverage,PairwiseAlignedFixedSubjectSummary-method compareStrings compareStrings,character,character-method compareStrings,XString,XString-method compareStrings,XStringSet,XStringSet-method compareStrings,AlignedXStringSet,AlignedXStringSet-method compareStrings,PairwiseAlignedFixedSubject,missing-method consensusMatrix consensusMatrix,character-method consensusMatrix,matrix-method consensusMatrix,list-method consensusMatrix,XStringSet-method consensusMatrix,XStringViews-method consensusMatrix,PairwiseAlignedFixedSubject-method consensusString consensusString,ANY-method consmat consmat,ANY-method
Keywords: methods
Description: Utility functions related to sequence alignment
URL: ../../../library/Biostrings/html/align-utils.html

Entry: alphabetFrequency
Aliases: alphabetFrequency alphabetFrequency,XString-method alphabetFrequency,DNAString-method alphabetFrequency,RNAString-method alphabetFrequency,XStringSet-method alphabetFrequency,DNAStringSet-method alphabetFrequency,RNAStringSet-method alphabetFrequency,XStringViews-method alphabetFrequency,MaskedXString-method hasOnlyBaseLetters hasOnlyBaseLetters,DNAString-method hasOnlyBaseLetters,DNAStringSet-method hasOnlyBaseLetters,RNAString-method hasOnlyBaseLetters,RNAStringSet-method hasOnlyBaseLetters,XStringViews-method hasOnlyBaseLetters,MaskedDNAString-method hasOnlyBaseLetters,MaskedRNAString-method uniqueLetters uniqueLetters,XString-method uniqueLetters,XStringSet-method uniqueLetters,XStringViews-method uniqueLetters,MaskedXString-method oligonucleotideFrequency oligonucleotideFrequency,DNAString-method oligonucleotideFrequency,RNAString-method oligonucleotideFrequency,XStringSet-method oligonucleotideFrequency,XStringViews-method oligonucleotideFrequency,MaskedXString-method dinucleotideFrequency trinucleotideFrequency oligonucleotideTransitions strrev mkAllStrings
Keywords: category
Description: Function to calculate the frequency of letters in a biological sequence and related functions
URL: ../../../library/Biostrings/html/alphabetFrequency.html

Entry: chartr
Aliases: chartr chartr,XString-method chartr,XStringSet-method chartr,XStringViews-method chartr,MaskedXString-method
Keywords: methods manip
Description: Translating letters of a sequence
URL: ../../../library/Biostrings/html/chartr.html

Entry: findPalindromes
Aliases: findPalindromes findPalindromes,XString-method findPalindromes,XStringViews-method findPalindromes,MaskedXString-method palindromeArmLength palindromeArmLength,XString-method palindromeArmLength,XStringViews-method palindromeLeftArm palindromeLeftArm,XString-method palindromeLeftArm,XStringViews-method palindromeRightArm palindromeRightArm,XString-method palindromeRightArm,XStringViews-method findComplementedPalindromes findComplementedPalindromes,DNAString-method findComplementedPalindromes,XStringViews-method findComplementedPalindromes,MaskedXString-method complementedPalindromeArmLength complementedPalindromeArmLength,DNAString-method complementedPalindromeArmLength,XStringViews-method complementedPalindromeLeftArm complementedPalindromeLeftArm,DNAString-method complementedPalindromeLeftArm,XStringViews-method complementedPalindromeRightArm complementedPalindromeRightArm,DNAString-method complementedPalindromeRightArm,XStringViews-method
Keywords: methods
Description: Searching a sequence for palindromes or complemented palindromes
URL: ../../../library/Biostrings/html/findPalindromes.html

Entry: gregexpr2
Aliases: gregexpr2
Keywords: manip
Description: A replacement for R standard gregexpr function
URL: ../../../library/Biostrings/html/gregexpr2.html

Entry: injectHardMask
Aliases: injectHardMask injectHardMask,XStringViews-method injectHardMask,MaskedXString-method
Keywords: utilities manip
Description: Injecting a hard mask in a sequence
URL: ../../../library/Biostrings/html/injectHardMask.html

Entry: letter
Aliases: letter letter,character-method letter,XString-method letter,XStringViews-method letter,MaskedXString-method
Keywords: methods
Description: Subsetting a string
URL: ../../../library/Biostrings/html/letter.html

Entry: maskMotif
Aliases: maskMotif maskMotif,MaskedXString,XString-method maskMotif,MaskedXString,character-method maskMotif,XString,ANY-method mask
Keywords: methods manip
Description: Masking by content (or by position)
URL: ../../../library/Biostrings/html/maskMotif.html

Entry: match-utils
Aliases: match-utils neditStartingAt neditEndingAt neditAt isMatchingStartingAt isMatchingEndingAt isMatchingAt neditStartingAt,character-method neditStartingAt,XString-method neditEndingAt,character-method neditEndingAt,XString-method isMatchingStartingAt,character-method isMatchingStartingAt,XString-method isMatchingEndingAt,character-method isMatchingEndingAt,XString-method mismatch mismatch,ANY,XStringViews-method nmatch nmatch,ANY,XStringViews-method nmismatch nmismatch,ANY,XStringViews-method coverage,XStringViews-method coverage,MaskedXString-method coverage,MIndex-method nmismatchStartingAt nmismatchEndingAt isMatching
Keywords: methods
Description: Utility functions related to pattern matching
URL: ../../../library/Biostrings/html/match-utils.html

Entry: matchLRPatterns
Aliases: matchLRPatterns matchLRPatterns,XString-method matchLRPatterns,XStringViews-method matchLRPatterns,MaskedXString-method
Keywords: methods
Description: Find paired matches in a sequence
URL: ../../../library/Biostrings/html/matchLRPatterns.html

Entry: matchPDict
Aliases: matchPDict-exact matchPDict matchPDict,XString-method matchPDict,XStringSet-method matchPDict,XStringViews-method matchPDict,MaskedXString-method countPDict countPDict,XString-method countPDict,XStringSet-method countPDict,XStringViews-method countPDict,MaskedXString-method whichPDict whichPDict,XString-method vmatchPDict vmatchPDict,ANY-method vmatchPDict,XString-method vmatchPDict,MaskedXString-method vcountPDict vcountPDict,XString-method vcountPDict,XStringSet-method vcountPDict,XStringViews-method vcountPDict,MaskedXString-method extractAllMatches
Keywords: methods
Description: Searching a sequence for patterns stored in a preprocessed dictionary
URL: ../../../library/Biostrings/html/matchPDict-exact.html

Entry: matchPDict-inexact
Aliases: matchPDict-inexact
Keywords: methods
Description: Inexact matching with matchPDict()/countPDict()/whichPDict()
URL: ../../../library/Biostrings/html/matchPDict-inexact.html

Entry: matchPWM
Aliases: maxWeights maxScore PWMscore matchPWM countPWM reverseComplement,matrix-method
Keywords: methods manip utilities
Description: A simple PWM matching function and related utilities
URL: ../../../library/Biostrings/html/matchPWM.html

Entry: matchPattern
Aliases: matchPattern matchPattern,character-method matchPattern,XString-method matchPattern,XStringSet-method matchPattern,XStringViews-method matchPattern,MaskedXString-method countPattern countPattern,character-method countPattern,XString-method countPattern,XStringSet-method countPattern,XStringViews-method countPattern,MaskedXString-method vmatchPattern vmatchPattern,character-method vmatchPattern,XString-method vmatchPattern,XStringSet-method vmatchPattern,XStringViews-method vmatchPattern,MaskedXString-method vcountPattern vcountPattern,character-method vcountPattern,XString-method vcountPattern,XStringSet-method vcountPattern,XStringViews-method vcountPattern,MaskedXString-method matchDNAPattern
Keywords: methods
Description: String searching functions
URL: ../../../library/Biostrings/html/matchPattern.html

Entry: matchProbePair
Aliases: matchProbePair matchProbePair,DNAString-method matchProbePair,XStringViews-method matchProbePair,MaskedDNAString-method
Keywords: methods
Description: Find "theoretical amplicons" mapped to a probe pair
URL: ../../../library/Biostrings/html/matchProbePair.html

Entry: needwunsQS
Aliases: needwunsQS needwunsQS,character,character-method needwunsQS,character,XString-method needwunsQS,XString,character-method needwunsQS,XString,XString-method print.needwunsQS alignScore.needwunsQS alignScore
Keywords: models methods
Description: (Deprecated) Needleman-Wunsch Global Alignment
URL: ../../../library/Biostrings/html/needwunsQS.html

Entry: pairwiseAlignment
Aliases: pairwiseAlignment pairwiseAlignment,character,character-method pairwiseAlignment,character,XString-method pairwiseAlignment,character,XStringSet-method pairwiseAlignment,character,QualityScaledXStringSet-method pairwiseAlignment,XString,character-method pairwiseAlignment,XString,XString-method pairwiseAlignment,XString,XStringSet-method pairwiseAlignment,XString,QualityScaledXStringSet-method pairwiseAlignment,XStringSet,character-method pairwiseAlignment,XStringSet,XString-method pairwiseAlignment,XStringSet,XStringSet-method pairwiseAlignment,XStringSet,QualityScaledXStringSet-method pairwiseAlignment,QualityScaledXStringSet,character-method pairwiseAlignment,QualityScaledXStringSet,XString-method pairwiseAlignment,QualityScaledXStringSet,XStringSet-method pairwiseAlignment,QualityScaledXStringSet,QualityScaledXStringSet-method
Keywords: models methods
Description: Optimal Pairwise Alignment
URL: ../../../library/Biostrings/html/pairwiseAlignment.html

Entry: phiX174Phage
Aliases: phiX174Phage srPhiX174 quPhiX174 wtPhiX174
Keywords: datasets
Description: Versions of bacteriophage phiX174 complete genome and sample short reads
URL: ../../../library/Biostrings/html/phiX174Phage.html

Entry: pid
Aliases: pid pid,PairwiseAlignedFixedSubject-method
Keywords: methods
Description: Percent Sequence Identity
URL: ../../../library/Biostrings/html/pid.html

Entry: pmatchPattern
Aliases: lcprefix lcprefix,character,character-method lcprefix,character,XString-method lcprefix,XString,character-method lcprefix,XString,XString-method lcsuffix lcsuffix,character,character-method lcsuffix,character,XString-method lcsuffix,XString,character-method lcsuffix,XString,XString-method lcsubstr lcsubstr,character,character-method lcsubstr,character,XString-method lcsubstr,XString,character-method lcsubstr,XString,XString-method pmatchPattern pmatchPattern,character-method pmatchPattern,XString-method pmatchPattern,XStringViews-method
Keywords: methods
Description: Longest Common Prefix/Suffix/Substring searching functions
URL: ../../../library/Biostrings/html/pmatchPattern.html

Entry: readFASTA
Aliases: fasta.info readFASTA writeFASTA
Keywords: utilities manip
Description: Functions to read/write FASTA formatted files
URL: ../../../library/Biostrings/html/readFASTA.html

Entry: replaceLetterAt
Aliases: replaceLetterAt replaceLetterAt,DNAString-method .inplaceReplaceLetterAt replaceLetterAtLoc
Keywords: utilities manip
Description: Replacing letters in a sequence at some specified locations
URL: ../../../library/Biostrings/html/replaceLetterAt.html

Entry: reverseComplement
Aliases: reverse,XString-method reverse,XStringSet-method reverse,XStringViews-method reverse,MaskedXString-method complement complement,DNAString-method complement,RNAString-method complement,DNAStringSet-method complement,RNAStringSet-method complement,XStringViews-method complement,MaskedDNAString-method complement,MaskedRNAString-method reverseComplement reverseComplement,DNAString-method reverseComplement,RNAString-method reverseComplement,DNAStringSet-method reverseComplement,RNAStringSet-method reverseComplement,XStringViews-method reverseComplement,MaskedDNAString-method reverseComplement,MaskedRNAString-method
Keywords: methods manip
Description: Sequence reversing and complementing
URL: ../../../library/Biostrings/html/reverse.html

Entry: stringDist
Aliases: stringDist stringDist,character-method stringDist,XStringSet-method stringDist,QualityScaledXStringSet-method
Keywords: character multivariate cluster
Description: String Distance/Alignment Score Matrix
URL: ../../../library/Biostrings/html/stringDist.html

Entry: subXString
Aliases: subXString subBString substr substr,XString-method substr,MaskedXString-method substring substring,XString-method substring,MaskedXString-method
Keywords: methods manip
Description: Fast substring extraction
URL: ../../../library/Biostrings/html/subXString.html

Entry: substitution.matrices
Aliases: substitution.matrices BLOSUM45 BLOSUM50 BLOSUM62 BLOSUM80 BLOSUM100 PAM30 PAM40 PAM70 PAM120 PAM250 nucleotideSubstitutionMatrix qualitySubstitutionMatrices errorSubstitutionMatrices
Keywords: utilities data datasets
Description: Scoring matrices
URL: ../../../library/Biostrings/html/substitution_matrices.html

Entry: toComplex
Aliases: toComplex toComplex,DNAString-method as.complex,DNAString-method
Keywords: methods
Description: Turning a DNA sequence into a vector of complex numbers
URL: ../../../library/Biostrings/html/toComplex.html

Entry: translate
Aliases: transcribe cDNA dna2rna rna2dna codons codons,DNAString-method codons,RNAString-method codons,MaskedDNAString-method codons,MaskedRNAString-method translate translate,DNAString-method translate,RNAString-method translate,DNAStringSet-method translate,RNAStringSet-method translate,MaskedDNAString-method translate,MaskedRNAString-method
Keywords: methods manip
Description: DNA/RNA transcription and translation
URL: ../../../library/Biostrings/html/translate.html

Entry: yeastSEQCHR1
Aliases: yeastSEQCHR1
Keywords: datasets
Description: An annotation data file for CHR1 in the yeastSEQ package
URL: ../../../library/Biostrings/html/yeastSEQCHR1.html
