# String objects representing biological sequences, and matching algorithms

## Documentation for package ‘Biostrings’ version 2.8.18

## User Guides and Package Vignettes

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## Help Pages

A B C D E F G H I L M N O P R S T U V W X Y misc

!=,BString,character-method | BString objects
!=,character,BString-method | BString objects
!=,character,XStringViews-method | The XStringViews class
!=,XString,XString-method | BString objects
!=,XString,XStringViews-method | The XStringViews class
!=,XStringViews,character-method | The XStringViews class
!=,XStringViews,XString-method | The XStringViews class
!=,XStringViews,XStringViews-method | The XStringViews class
$,MIndex-method | Searching a sequence for patterns stored in a dictionary
.inplaceReplaceLetterAtLoc | Replacing letters in a sequence at some specified locations
==,BString,character-method | BString objects
==,character,BString-method | BString objects
==,character,XStringViews-method | The XStringViews class
==,XString,XString-method | BString objects
==,XString,XStringViews-method | The XStringViews class
==,XStringViews,character-method | The XStringViews class
==,XStringViews,XString-method | The XStringViews class
==,XStringViews,XStringViews-method | The XStringViews class

## -- A --

AAString | AAString objects
AAString-class | AAString objects
AAStringList | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
AAStringList,ANY-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
AAStringList,character-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
AAStringList,vector-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
AAStringList,XStringList-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
AAStringList-class | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
AAStringSet | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
AAStringSet-class | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
AA_ALPHABET | AAString objects
active | MaskCollection objects
active,MaskCollection-method | MaskCollection objects
active<-,MaskCollection-method | MaskCollection objects
ACtree | PDict objects
ACtree-class | PDict objects
adjacentViews | Basic functions for creating or modifying XStringViews objects
align1 | XStringAlign objects
align1,XStringAlign-method | XStringAlign objects
align2 | XStringAlign objects
align2,XStringAlign-method | XStringAlign objects
alignScore | (Deprecated) Needleman-Wunsch Global Alignment
alphabet | BString objects
alphabet,AAString-method | AAString objects
alphabet,BString-method | BString objects
alphabet,DNAString-method | DNAString objects
alphabet,MaskedXString-method | MaskedXString objects
alphabet,RNAString-method | RNAString objects
alphabet,XStringAlign-method | XStringAlign objects
alphabet,XStringSet-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
alphabet,XStringViews-method | The XStringViews class
alphabetFrequency | Functions to calculate the frequency of letters in a biological sequence
alphabetFrequency,DNAString-method | Functions to calculate the frequency of letters in a biological sequence
alphabetFrequency,DNAStringSet-method | Functions to calculate the frequency of letters in a biological sequence
alphabetFrequency,MaskedXString-method | Functions to calculate the frequency of letters in a biological sequence
alphabetFrequency,RNAString-method | Functions to calculate the frequency of letters in a biological sequence
alphabetFrequency,RNAStringSet-method | Functions to calculate the frequency of letters in a biological sequence
alphabetFrequency,XString-method | Functions to calculate the frequency of letters in a biological sequence
alphabetFrequency,XStringSet-method | Functions to calculate the frequency of letters in a biological sequence
alphabetFrequency,XStringViews-method | Functions to calculate the frequency of letters in a biological sequence
AMINO_ACID_CODE | The Single-Letter Amino Acid Code
append,MaskCollection-method | MaskCollection objects
as.character,MaskedXString-method | MaskedXString objects
as.character,XString-method | BString objects
as.character,XStringAlign-method | XStringAlign objects
as.character,XStringSet-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
as.character,XStringViews-method | The XStringViews class
as.complex,DNAString-method | Converting a DNAString to a vector of complexes
as.data.frame,IRanges-method | IRanges and NormalIRanges objects
as.list,XStringList-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
as.list,XStringSet-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
as.list,XStringViews-method | The XStringViews class
as.matrix,ACtree-method | PDict objects
as.matrix,IRanges-method | IRanges and NormalIRanges objects
as.matrix,XStringViews-method | The XStringViews class

## -- B --

BLOSUM100 | Scoring matrices
BLOSUM45 | Scoring matrices
BLOSUM50 | Scoring matrices
BLOSUM62 | Scoring matrices
BLOSUM80 | Scoring matrices
BOC2_SubjectString | BOC_SubjectString and BOC2_SubjectString objects
BOC2_SubjectString-class | BOC_SubjectString and BOC2_SubjectString objects
BOC_SubjectString | BOC_SubjectString and BOC2_SubjectString objects
BOC_SubjectString-class | BOC_SubjectString and BOC2_SubjectString objects
BString | BString objects
BString-class | BString objects
BStringList | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
BStringList,ANY-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
BStringList,character-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
BStringList,vector-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
BStringList,XStringList-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
BStringList-class | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
BStringSet | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
BStringSet-class | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
BStringViews | Basic functions for creating or modifying XStringViews objects
BStringViews,ANY-method | Basic functions for creating or modifying XStringViews objects
BStringViews,file-method | Basic functions for creating or modifying XStringViews objects
BStringViews,XString-method | Basic functions for creating or modifying XStringViews objects
BStringViews,XStringViews-method | Basic functions for creating or modifying XStringViews objects
ByName_MIndex-class | Searching a sequence for patterns stored in a dictionary
ByPos_MIndex-class | Searching a sequence for patterns stored in a dictionary

## -- C --

cDNA | Sequence reversing and complementing
CharacterToFASTArecords | Read/write an XStringSet or XStringViews object from/to a file
chartr | Translating letters of a sequence
chartr,MaskedXString-method | Translating letters of a sequence
chartr,XString-method | Translating letters of a sequence
chartr,XStringSet-method | Translating letters of a sequence
chartr,XStringViews-method | Translating letters of a sequence
class:AAString | AAString objects
class:AAStringList | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:AAStringSet | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:ACtree | PDict objects
class:BOC2_SubjectString | BOC_SubjectString and BOC2_SubjectString objects
class:BOC_SubjectString | BOC_SubjectString and BOC2_SubjectString objects
class:BString | BString objects
class:BStringList | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:BStringSet | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:ByName_MIndex | Searching a sequence for patterns stored in a dictionary
class:ByPos_MIndex | Searching a sequence for patterns stored in a dictionary
class:CWdna_PDict | PDict objects
class:DNAString | DNAString objects
class:DNAStringList | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:DNAStringSet | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:Dups | PDict objects
class:IRanges | IRanges and NormalIRanges objects
class:LockedIRanges | IRanges and NormalIRanges objects
class:MaskCollection | MaskCollection objects
class:MaskedAAString | MaskedXString objects
class:MaskedBString | MaskedXString objects
class:MaskedDNAString | MaskedXString objects
class:MaskedRNAString | MaskedXString objects
class:MaskedXString | MaskedXString objects
class:MIndex | Searching a sequence for patterns stored in a dictionary
class:NormalIRanges | IRanges and NormalIRanges objects
class:PDict | PDict objects
class:RNAString | RNAString objects
class:RNAStringList | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:RNAStringSet | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:TBdna_PDict | PDict objects
class:UnlockedIRanges | IRanges and NormalIRanges objects
class:Views | IRanges and NormalIRanges objects
class:XString | BString objects
class:XStringAlign | XStringAlign objects
class:XStringList | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:XStringPartialMatches | XStringPartialMatches objects
class:XStringSet | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:XStringViews | The XStringViews class
coerce,AAString,MaskedAAString-method | MaskedXString objects
coerce,BString,MaskedBString-method | MaskedXString objects
coerce,DNAString,MaskedDNAString-method | MaskedXString objects
coerce,IRanges,NormalIRanges-method | IRanges and NormalIRanges objects
coerce,LockedIRanges,NormalIRanges-method | IRanges and NormalIRanges objects
coerce,MaskCollection,NormalIRanges-method | MaskCollection objects
coerce,MaskedAAString,AAString-method | MaskedXString objects
coerce,MaskedBString,BString-method | MaskedXString objects
coerce,MaskedDNAString,DNAString-method | MaskedXString objects
coerce,MaskedRNAString,RNAString-method | MaskedXString objects
coerce,MaskedXString,MaskCollection-method | MaskedXString objects
coerce,MaskedXString,NormalIRanges-method | MaskedXString objects
coerce,MaskedXString,XStringViews-method | MaskedXString objects
coerce,RNAString,MaskedRNAString-method | MaskedXString objects
coerce,UnlockedIRanges,NormalIRanges-method | IRanges and NormalIRanges objects
coerce,Views,NormalIRanges-method | IRanges and NormalIRanges objects
complement | Sequence reversing and complementing
complement,DNAString-method | Sequence reversing and complementing
complement,DNAStringSet-method | Sequence reversing and complementing
complement,MaskedDNAString-method | Sequence reversing and complementing
complement,MaskedRNAString-method | Sequence reversing and complementing
complement,RNAString-method | Sequence reversing and complementing
complement,RNAStringSet-method | Sequence reversing and complementing
complement,XStringViews-method | Sequence reversing and complementing
complementedPalindromeArmLength | Searching a sequence for palindromes or complemented palindromes
complementedPalindromeArmLength,DNAString-method | Searching a sequence for palindromes or complemented palindromes
complementedPalindromeArmLength,XStringViews-method | Searching a sequence for palindromes or complemented palindromes
complementedPalindromeLeftArm | Searching a sequence for palindromes or complemented palindromes
complementedPalindromeLeftArm,DNAString-method | Searching a sequence for palindromes or complemented palindromes
complementedPalindromeLeftArm,XStringViews-method | Searching a sequence for palindromes or complemented palindromes
complementedPalindromeRightArm | Searching a sequence for palindromes or complemented palindromes
complementedPalindromeRightArm,DNAString-method | Searching a sequence for palindromes or complemented palindromes
complementedPalindromeRightArm,XStringViews-method | Searching a sequence for palindromes or complemented palindromes
consmat | Utility functions related to sequence alignment
consmat,character-method | Utility functions related to sequence alignment
consmat,list-method | Utility functions related to sequence alignment
consmat,matrix-method | Utility functions related to sequence alignment
consmat,XStringAlign-method | Utility functions related to sequence alignment
consmat,XStringSet-method | Utility functions related to sequence alignment
consmat,XStringViews-method | Utility functions related to sequence alignment
countIndex | Searching a sequence for patterns stored in a dictionary
countIndex,ByName_MIndex-method | Searching a sequence for patterns stored in a dictionary
countIndex,ByPos_MIndex-method | Searching a sequence for patterns stored in a dictionary
countIndex,MIndex-method | Searching a sequence for patterns stored in a dictionary
countPattern | String searching functions
countPattern,BOC2_SubjectString-method | BOC_SubjectString and BOC2_SubjectString objects
countPattern,character-method | String searching functions
countPattern,MaskedXString-method | String searching functions
countPattern,XString-method | String searching functions
countPattern,XStringViews-method | String searching functions
countPDict | Searching a sequence for patterns stored in a dictionary
countPDict,MaskedXString-method | Searching a sequence for patterns stored in a dictionary
countPDict,XString-method | Searching a sequence for patterns stored in a dictionary
countPDict,XStringViews-method | Searching a sequence for patterns stored in a dictionary
countPWM | A simple PWM matching function and related utilities
coverage | Utility functions related to pattern matching
coverage,IRanges-method | Utility functions related to pattern matching
coverage,MaskCollection-method | Utility functions related to pattern matching
coverage,MaskedXString-method | Utility functions related to pattern matching
coverage,MIndex-method | Utility functions related to pattern matching
coverage,XStringViews-method | Utility functions related to pattern matching
CWdna_PDict | PDict objects
CWdna_PDict-class | PDict objects

## -- D --

desc | IRanges and NormalIRanges objects
dinucleotideFrequency | Functions to calculate the frequency of letters in a biological sequence
dna2rna | Sequence reversing and complementing
DNAString | DNAString objects
DNAString-class | DNAString objects
DNAStringList | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
DNAStringList,ANY-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
DNAStringList,character-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
DNAStringList,vector-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
DNAStringList,XStringList-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
DNAStringList-class | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
DNAStringSet | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
DNAStringSet-class | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
DNA_ALPHABET | DNAString objects
duplicated,CWdna_PDict-method | PDict objects
duplicated,Dups-method | PDict objects
duplicated,IRanges-method | IRanges and NormalIRanges objects
duplicated,TBdna_PDict-method | PDict objects
Dups | PDict objects
Dups-class | PDict objects

## -- E --

end,IRanges-method | IRanges and NormalIRanges objects
end<-,UnlockedIRanges-method | IRanges and NormalIRanges objects
endIndex | Searching a sequence for patterns stored in a dictionary
endIndex,ByName_MIndex-method | Searching a sequence for patterns stored in a dictionary
endIndex,ByPos_MIndex-method | Searching a sequence for patterns stored in a dictionary
extractAllMatches | Searching a sequence for patterns stored in a dictionary

## -- F --

FASTArecordsToBStringViews | Read/write an XStringSet or XStringViews object from/to a file
FASTArecordsToCharacter | Read/write an XStringSet or XStringViews object from/to a file
FASTArecordsToXStringViews | Read/write an XStringSet or XStringViews object from/to a file
findComplementedPalindromes | Searching a sequence for palindromes or complemented palindromes
findComplementedPalindromes,DNAString-method | Searching a sequence for palindromes or complemented palindromes
findComplementedPalindromes,MaskedXString-method | Searching a sequence for palindromes or complemented palindromes
findComplementedPalindromes,XStringViews-method | Searching a sequence for palindromes or complemented palindromes
findPalindromes | Searching a sequence for palindromes or complemented palindromes
findPalindromes,MaskedXString-method | Searching a sequence for palindromes or complemented palindromes
findPalindromes,XString-method | Searching a sequence for palindromes or complemented palindromes
findPalindromes,XStringViews-method | Searching a sequence for palindromes or complemented palindromes
first | IRanges and NormalIRanges objects
first,IRanges-method | IRanges and NormalIRanges objects

## -- G --

gaps | IRanges utility functions
gaps,IRanges-method | IRanges utility functions
gaps,MaskCollection-method | MaskCollection objects
gaps,MaskedXString-method | MaskedXString objects
gaps,XStringViews-method | Basic functions for creating or modifying XStringViews objects
GENETIC_CODE | The Standard Genetic Code
gregexpr2 | A replacement for R standard gregexpr function

## -- H --

head,TBdna_PDict-method | PDict objects

## -- I --

initialize,AAStringList-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
initialize,ACtree-method | PDict objects
initialize,BOC2_SubjectString-method | BOC_SubjectString and BOC2_SubjectString objects
initialize,BOC_SubjectString-method | BOC_SubjectString and BOC2_SubjectString objects
initialize,BStringList-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
initialize,CWdna_PDict-method | PDict objects
initialize,DNAStringList-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
initialize,IRanges-method | IRanges and NormalIRanges objects
initialize,NormalIRanges-method | IRanges and NormalIRanges objects
initialize,RNAStringList-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
initialize,TBdna_PDict-method | PDict objects
initialize,Views-method | IRanges and NormalIRanges objects
initialize,XStringAlign-method | XStringAlign objects
initialize,XStringSet-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
initialize,XStringViews-method | The XStringViews class
injectHardMask | Injecting a hard mask in a sequence
injectHardMask,MaskedXString-method | Injecting a hard mask in a sequence
injectHardMask,XStringViews-method | Injecting a hard mask in a sequence
intToAdjacentRanges | IRanges utility functions
intToRanges | IRanges utility functions
IRanges | IRanges and NormalIRanges objects
IRanges-class | IRanges and NormalIRanges objects
IRanges-utils | IRanges utility functions
isEmpty | IRanges and NormalIRanges objects
isEmpty,IRanges-method | IRanges and NormalIRanges objects
isEmpty,MaskCollection-method | MaskCollection objects
isEmpty,NormalIRanges-method | IRanges and NormalIRanges objects
isMatching | Utility functions related to pattern matching
isMatching,character-method | Utility functions related to pattern matching
isMatching,XString-method | Utility functions related to pattern matching
isNormal | IRanges and NormalIRanges objects
isNormal,IRanges-method | IRanges and NormalIRanges objects
IUPAC_CODE_MAP | The IUPAC Extended Genetic Alphabet

## -- L --

last | IRanges and NormalIRanges objects
last,IRanges-method | IRanges and NormalIRanges objects
lcprefix | Longest Common Prefix/Suffix/Substring searching functions
lcprefix,character,character-method | Longest Common Prefix/Suffix/Substring searching functions
lcprefix,character,XString-method | Longest Common Prefix/Suffix/Substring searching functions
lcprefix,XString,character-method | Longest Common Prefix/Suffix/Substring searching functions
lcprefix,XString,XString-method | Longest Common Prefix/Suffix/Substring searching functions
lcsubstr | Longest Common Prefix/Suffix/Substring searching functions
lcsubstr,character,character-method | Longest Common Prefix/Suffix/Substring searching functions
lcsubstr,character,XString-method | Longest Common Prefix/Suffix/Substring searching functions
lcsubstr,XString,character-method | Longest Common Prefix/Suffix/Substring searching functions
lcsubstr,XString,XString-method | Longest Common Prefix/Suffix/Substring searching functions
lcsuffix | Longest Common Prefix/Suffix/Substring searching functions
lcsuffix,character,character-method | Longest Common Prefix/Suffix/Substring searching functions
lcsuffix,character,XString-method | Longest Common Prefix/Suffix/Substring searching functions
lcsuffix,XString,character-method | Longest Common Prefix/Suffix/Substring searching functions
lcsuffix,XString,XString-method | Longest Common Prefix/Suffix/Substring searching functions
length,ACtree-method | PDict objects
length,ByName_MIndex-method | Searching a sequence for patterns stored in a dictionary
length,ByPos_MIndex-method | Searching a sequence for patterns stored in a dictionary
length,CWdna_PDict-method | PDict objects
length,Dups-method | PDict objects
length,IRanges-method | IRanges and NormalIRanges objects
length,MaskCollection-method | MaskCollection objects
length,MaskedXString-method | MaskedXString objects
length,XString-method | BString objects
length,XStringAlign-method | XStringAlign objects
length,XStringList-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
letter | Subsetting a string
letter,character-method | Subsetting a string
letter,MaskedXString-method | Subsetting a string
letter,XString-method | Subsetting a string
letter,XStringViews-method | Subsetting a string
LockedIRanges | IRanges and NormalIRanges objects
LockedIRanges-class | IRanges and NormalIRanges objects

## -- M --

Mask | MaskCollection objects
mask | Masking by content (or by position)
MaskCollection | MaskCollection objects
MaskCollection-class | MaskCollection objects
MaskedAAString | MaskedXString objects
MaskedAAString-class | MaskedXString objects
MaskedBString | MaskedXString objects
MaskedBString-class | MaskedXString objects
MaskedDNAString | MaskedXString objects
MaskedDNAString-class | MaskedXString objects
maskedratio | MaskCollection objects
maskedratio,MaskCollection-method | MaskCollection objects
maskedratio,MaskedXString-method | MaskedXString objects
MaskedRNAString | MaskedXString objects
MaskedRNAString-class | MaskedXString objects
maskedwidth | MaskCollection objects
maskedwidth,MaskCollection-method | MaskCollection objects
maskedwidth,MaskedXString-method | MaskedXString objects
MaskedXString | MaskedXString objects
MaskedXString-class | MaskedXString objects
maskMotif | Masking by content (or by position)
maskMotif,MaskedXString,character-method | Masking by content (or by position)
maskMotif,MaskedXString,XString-method | Masking by content (or by position)
maskMotif,XString,ANY-method | Masking by content (or by position)
masks | MaskedXString objects
masks,MaskedXString-method | MaskedXString objects
masks,XString-method | MaskedXString objects
masks<-,MaskedXString,MaskCollection-method | MaskedXString objects
masks<-,MaskedXString,NULL-method | MaskedXString objects
masks<-,XString,ANY-method | MaskedXString objects
masks<-,XString,NULL-method | MaskedXString objects
match-utils | Utility functions related to pattern matching
matchDNAPattern | String searching functions
matchLRPatterns | Find patterns defined by a left and a right part in a sequence
matchLRPatterns,MaskedXString-method | Find patterns defined by a left and a right part in a sequence
matchLRPatterns,XString-method | Find patterns defined by a left and a right part in a sequence
matchLRPatterns,XStringViews-method | Find patterns defined by a left and a right part in a sequence
matchPattern | String searching functions
matchPattern,BOC2_SubjectString-method | BOC_SubjectString and BOC2_SubjectString objects
matchPattern,BOC_SubjectString-method | BOC_SubjectString and BOC2_SubjectString objects
matchPattern,character-method | String searching functions
matchPattern,MaskedXString-method | String searching functions
matchPattern,XString-method | String searching functions
matchPattern,XStringViews-method | String searching functions
matchPDict | Searching a sequence for patterns stored in a dictionary
matchPDict,MaskedXString-method | Searching a sequence for patterns stored in a dictionary
matchPDict,XString-method | Searching a sequence for patterns stored in a dictionary
matchPDict,XStringViews-method | Searching a sequence for patterns stored in a dictionary
matchPDict-exact | Searching a sequence for patterns stored in a dictionary
matchPDict-inexact | Inexact matching with matchPDict()
matchProbePair | Find "theoretical amplicons" mapped to a probe pair
matchProbePair,DNAString-method | Find "theoretical amplicons" mapped to a probe pair
matchProbePair,MaskedDNAString-method | Find "theoretical amplicons" mapped to a probe pair
matchProbePair,XStringViews-method | Find "theoretical amplicons" mapped to a probe pair
matchPWM | A simple PWM matching function and related utilities
max,MaskCollection-method | MaskCollection objects
max,NormalIRanges-method | IRanges and NormalIRanges objects
maxScore | A simple PWM matching function and related utilities
maxWeights | A simple PWM matching function and related utilities
mergeIUPACLetters | The IUPAC Extended Genetic Alphabet
min,MaskCollection-method | MaskCollection objects
min,NormalIRanges-method | IRanges and NormalIRanges objects
MIndex | Searching a sequence for patterns stored in a dictionary
MIndex-class | Searching a sequence for patterns stored in a dictionary
mismatch | Utility functions related to pattern matching
mismatch,XStringViews-method | Utility functions related to pattern matching
mkAllStrings | Functions to calculate the frequency of letters in a biological sequence

## -- N --

names,ByName_MIndex-method | Searching a sequence for patterns stored in a dictionary
names,ByPos_MIndex-method | Searching a sequence for patterns stored in a dictionary
names,CWdna_PDict-method | PDict objects
names,IRanges-method | IRanges and NormalIRanges objects
names,MaskCollection-method | MaskCollection objects
names,XStringList-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
names<-,IRanges-method | IRanges and NormalIRanges objects
names<-,MaskCollection-method | MaskCollection objects
names<-,XStringList-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
narrow | IRanges utility functions
narrow,IRanges-method | IRanges utility functions
narrow,MaskCollection-method | MaskCollection objects
narrow,NormalIRanges-method | IRanges utility functions
narrow,numeric-method | IRanges utility functions
narrow,XStringViews-method | Basic functions for creating or modifying XStringViews objects
nchar,MaskedXString-method | MaskedXString objects
nchar,XString-method | BString objects
nchar,XStringAlign-method | XStringAlign objects
nchar,XStringList-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
nchar,XStringSet-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
nchar,XStringViews-method | The XStringViews class
needwunsQS | (Deprecated) Needleman-Wunsch Global Alignment
needwunsQS,character,character-method | (Deprecated) Needleman-Wunsch Global Alignment
needwunsQS,character,XString-method | (Deprecated) Needleman-Wunsch Global Alignment
needwunsQS,XString,character-method | (Deprecated) Needleman-Wunsch Global Alignment
needwunsQS,XString,XString-method | (Deprecated) Needleman-Wunsch Global Alignment
nir_list | MaskCollection objects
nir_list,MaskCollection-method | MaskCollection objects
nmismatchEndingAt | Utility functions related to pattern matching
nmismatchEndingAt,character-method | Utility functions related to pattern matching
nmismatchEndingAt,XString-method | Utility functions related to pattern matching
nmismatchStartingAt | Utility functions related to pattern matching
nmismatchStartingAt,character-method | Utility functions related to pattern matching
nmismatchStartingAt,XString-method | Utility functions related to pattern matching
NormalIRanges | IRanges and NormalIRanges objects
NormalIRanges-class | IRanges and NormalIRanges objects

## -- O --

oligonucleotideFrequency | Functions to calculate the frequency of letters in a biological sequence
oligonucleotideFrequency,DNAString-method | Functions to calculate the frequency of letters in a biological sequence
oligonucleotideFrequency,MaskedXString-method | Functions to calculate the frequency of letters in a biological sequence
oligonucleotideFrequency,RNAString-method | Functions to calculate the frequency of letters in a biological sequence
oligonucleotideFrequency,XStringSet-method | Functions to calculate the frequency of letters in a biological sequence
oligonucleotideFrequency,XStringViews-method | Functions to calculate the frequency of letters in a biological sequence

## -- P --

pairwiseAlignment | Optimal Pairwise Alignment
pairwiseAlignment,character,character-method | Optimal Pairwise Alignment
pairwiseAlignment,character,XString-method | Optimal Pairwise Alignment
pairwiseAlignment,XString,character-method | Optimal Pairwise Alignment
pairwiseAlignment,XString,XString-method | Optimal Pairwise Alignment
palindromeArmLength | Searching a sequence for palindromes or complemented palindromes
palindromeArmLength,XString-method | Searching a sequence for palindromes or complemented palindromes
palindromeArmLength,XStringViews-method | Searching a sequence for palindromes or complemented palindromes
palindromeLeftArm | Searching a sequence for palindromes or complemented palindromes
palindromeLeftArm,XString-method | Searching a sequence for palindromes or complemented palindromes
palindromeLeftArm,XStringViews-method | Searching a sequence for palindromes or complemented palindromes
palindromeRightArm | Searching a sequence for palindromes or complemented palindromes
palindromeRightArm,XString-method | Searching a sequence for palindromes or complemented palindromes
palindromeRightArm,XStringViews-method | Searching a sequence for palindromes or complemented palindromes
PAM120 | Scoring matrices
PAM250 | Scoring matrices
PAM30 | Scoring matrices
PAM40 | Scoring matrices
PAM70 | Scoring matrices
pattern | XStringPartialMatches objects
pattern,XStringPartialMatches-method | XStringPartialMatches objects
patternFrequency | PDict objects
patternFrequency,CWdna_PDict-method | PDict objects
patternFrequency,TBdna_PDict-method | PDict objects
PDict | PDict objects
PDict,AsIs-method | PDict objects
PDict,character-method | PDict objects
PDict,DNAStringSet-method | PDict objects
PDict,XStringViews-method | PDict objects
PDict-class | PDict objects
pmatchPattern | Longest Common Prefix/Suffix/Substring searching functions
pmatchPattern,character-method | Longest Common Prefix/Suffix/Substring searching functions
pmatchPattern,XString-method | Longest Common Prefix/Suffix/Substring searching functions
pmatchPattern,XStringViews-method | Longest Common Prefix/Suffix/Substring searching functions
print.needwunsQS | (Deprecated) Needleman-Wunsch Global Alignment
PWMscore | A simple PWM matching function and related utilities

## -- R --

read.AAStringSet | Read/write an XStringSet or XStringViews object from/to a file
read.agpMask | Read a mask from a file
read.BStringSet | Read/write an XStringSet or XStringViews object from/to a file
read.BStringViews | Read/write an XStringSet or XStringViews object from/to a file
read.DNAStringSet | Read/write an XStringSet or XStringViews object from/to a file
read.gapMask | Read a mask from a file
read.liftMask | Read a mask from a file
read.Mask | Read a mask from a file
read.rmMask | Read a mask from a file
read.RNAStringSet | Read/write an XStringSet or XStringViews object from/to a file
read.trfMask | Read a mask from a file
read.XStringViews | Read/write an XStringSet or XStringViews object from/to a file
readFASTA | Functions to read/write FASTA formatted files
reduce | IRanges utility functions
reduce,IRanges-method | IRanges utility functions
reduce,MaskCollection-method | MaskCollection objects
reduce,MaskedXString-method | MaskedXString objects
replaceLetterAtLoc | Replacing letters in a sequence at some specified locations
replaceLetterAtLoc,DNAString-method | Replacing letters in a sequence at some specified locations
restrict | IRanges utility functions
restrict,IRanges-method | IRanges utility functions
restrict,XStringViews-method | Basic functions for creating or modifying XStringViews objects
reverse | Sequence reversing and complementing
reverse,IRanges-method | Sequence reversing and complementing
reverse,MaskCollection-method | Sequence reversing and complementing
reverse,MaskedXString-method | Sequence reversing and complementing
reverse,NormalIRanges-method | Sequence reversing and complementing
reverse,XString-method | Sequence reversing and complementing
reverse,XStringSet-method | Sequence reversing and complementing
reverse,XStringViews-method | Sequence reversing and complementing
reverseComplement | Sequence reversing and complementing
reverseComplement,DNAString-method | Sequence reversing and complementing
reverseComplement,DNAStringSet-method | Sequence reversing and complementing
reverseComplement,MaskedDNAString-method | Sequence reversing and complementing
reverseComplement,MaskedRNAString-method | Sequence reversing and complementing
reverseComplement,matrix-method | A simple PWM matching function and related utilities
reverseComplement,RNAString-method | Sequence reversing and complementing
reverseComplement,RNAStringSet-method | Sequence reversing and complementing
reverseComplement,XStringViews-method | Sequence reversing and complementing
rna2dna | Sequence reversing and complementing
RNAString | RNAString objects
RNAString-class | RNAString objects
RNAStringList | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
RNAStringList,ANY-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
RNAStringList,character-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
RNAStringList,vector-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
RNAStringList,XStringList-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
RNAStringList-class | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
RNAStringSet | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
RNAStringSet-class | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
RNA_ALPHABET | RNAString objects

## -- S --

score | XStringAlign objects
score,XStringAlign-method | XStringAlign objects
shift | IRanges utility functions
shift,IRanges-method | IRanges utility functions
show,ACtree-method | PDict objects
show,ByName_MIndex-method | Searching a sequence for patterns stored in a dictionary
show,ByPos_MIndex-method | Searching a sequence for patterns stored in a dictionary
show,CWdna_PDict-method | PDict objects
show,IRanges-method | IRanges and NormalIRanges objects
show,MaskCollection-method | MaskCollection objects
show,MaskedXString-method | MaskedXString objects
show,TBdna_PDict-method | PDict objects
show,XString-method | BString objects
show,XStringAlign-method | XStringAlign objects
show,XStringList-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
show,XStringPartialMatches-method | XStringPartialMatches objects
show,XStringSet-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
show,XStringViews-method | The XStringViews class
start,IRanges-method | IRanges and NormalIRanges objects
start<-,UnlockedIRanges-method | IRanges and NormalIRanges objects
startIndex | Searching a sequence for patterns stored in a dictionary
startIndex,ByName_MIndex-method | Searching a sequence for patterns stored in a dictionary
startIndex,ByPos_MIndex-method | Searching a sequence for patterns stored in a dictionary
startIndex,MIndex-method | Searching a sequence for patterns stored in a dictionary
strrev | Functions to calculate the frequency of letters in a biological sequence
subBString | Fast substring extraction
subject | The XStringViews class
subject,XStringViews-method | The XStringViews class
subpatterns | XStringPartialMatches objects
subpatterns,XStringPartialMatches-method | XStringPartialMatches objects
subseq | BString objects
subseq,MaskedXString-method | MaskedXString objects
subseq,XString-method | BString objects
substitution.matrices | Scoring matrices
substr | Fast substring extraction
substr,XString-method | Fast substring extraction
substring | Fast substring extraction
substring,XString-method | Fast substring extraction
subviews | Basic functions for creating or modifying XStringViews objects
subXString | Fast substring extraction

## -- T --

tail,TBdna_PDict-method | PDict objects
TBdna_PDict | PDict objects
TBdna_PDict-class | PDict objects
toComplex | Converting a DNAString to a vector of complexes
toComplex,DNAString-method | Converting a DNAString to a vector of complexes
toNormalIRanges | IRanges utility functions
toString,MaskedXString-method | MaskedXString objects
toString,XString-method | BString objects
toString,XStringViews-method | The XStringViews class
transcribe | Sequence reversing and complementing
trim | Basic functions for creating or modifying XStringViews objects
trinucleotideFrequency | Functions to calculate the frequency of letters in a biological sequence
type | XStringAlign objects
type,XStringAlign-method | XStringAlign objects

## -- U --

unlist | Searching a sequence for patterns stored in a dictionary
unlist,MIndex-method | Searching a sequence for patterns stored in a dictionary
UnlockedIRanges | IRanges and NormalIRanges objects
UnlockedIRanges-class | IRanges and NormalIRanges objects
unmasked | MaskedXString objects
unmasked,MaskedXString-method | MaskedXString objects
update,UnlockedIRanges-method | IRanges and NormalIRanges objects

## -- V --

vcountPattern | String searching functions
vcountPattern,character-method | String searching functions
vcountPattern,XStringSet-method | String searching functions
Views | IRanges and NormalIRanges objects
views | Basic functions for creating or modifying XStringViews objects
Views-class | IRanges and NormalIRanges objects

## -- W --

whichFirstNotNormal | IRanges and NormalIRanges objects
whichFirstNotNormal,IRanges-method | IRanges and NormalIRanges objects
width | IRanges and NormalIRanges objects
width,CWdna_PDict-method | PDict objects
width,IRanges-method | IRanges and NormalIRanges objects
width,MaskCollection-method | MaskCollection objects
width,XStringList-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
width<-,UnlockedIRanges-method | IRanges and NormalIRanges objects
width<-,XStringViews-method | The XStringViews class
write.BStringViews | Read/write an XStringSet or XStringViews object from/to a file
write.XStringSet | Read/write an XStringSet or XStringViews object from/to a file
write.XStringViews | Read/write an XStringSet or XStringViews object from/to a file
writeFASTA | Functions to read/write FASTA formatted files

## -- X --

XString | BString objects
XString,AsIs-method | BString objects
XString,character-method | BString objects
XString,MaskedXString-method | MaskedXString objects
XString,XString-method | BString objects
XString-class | BString objects
XStringAlign | XStringAlign objects
XStringAlign-class | XStringAlign objects
XStringList | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
XStringList-class | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
XStringPartialMatches-class | XStringPartialMatches objects
XStringSet | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
XStringSet,AsIs-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
XStringSet,character-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
XStringSet,XString-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
XStringSet,XStringSet-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
XStringSet,XStringViews-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
XStringSet-class | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
XStringSetToFASTArecords | Read/write an XStringSet or XStringViews object from/to a file
XStringViews | Basic functions for creating or modifying XStringViews objects
XStringViews,ANY-method | Basic functions for creating or modifying XStringViews objects
XStringViews,file-method | Basic functions for creating or modifying XStringViews objects
XStringViews,XString-method | Basic functions for creating or modifying XStringViews objects
XStringViews,XStringViews-method | Basic functions for creating or modifying XStringViews objects
XStringViews-class | The XStringViews class
XStringViews-constructors | Basic functions for creating or modifying XStringViews objects

## -- Y --

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

## -- misc --

[,ACtree-method | PDict objects
[,IRanges-method | IRanges and NormalIRanges objects
[,MaskCollection-method | MaskCollection objects
[,XString-method | BString objects
[,XStringList-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
[,XStringPartialMatches-method | XStringPartialMatches objects
[<-,IRanges-method | IRanges and NormalIRanges objects
[<-,MaskCollection-method | MaskCollection objects
[<-,XString-method | BString objects
[<-,XStringList-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
[[,ByName_MIndex-method | Searching a sequence for patterns stored in a dictionary
[[,ByPos_MIndex-method | Searching a sequence for patterns stored in a dictionary
[[,MaskCollection-method | MaskCollection objects
[[,MIndex-method | Searching a sequence for patterns stored in a dictionary
[[,XStringList-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
[[,XStringSet-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
[[,XStringViews-method | The XStringViews class
[[<-,MaskCollection-method | MaskCollection objects
[[<-,XStringList-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
[[<-,XStringSet-method | BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
[[<-,XStringViews-method | The XStringViews class