!=,BString,BString-method	BString-class
!=,BString,BStringViews-method	BStringViews-class
!=,BString,character-method	BString-class
!=,BStringViews,BString-method	BStringViews-class
!=,BStringViews,BStringViews-method	BStringViews-class
!=,BStringViews,character-method	BStringViews-class
!=,character,BString-method	BString-class
!=,character,BStringViews-method	BStringViews-class
!=,XInteger,XInteger-method	Biostrings-internals
!=,XRaw,XRaw-method	Biostrings-internals
==,BString,BString-method	BString-class
==,BString,BStringViews-method	BStringViews-class
==,BString,character-method	BString-class
==,BStringViews,BString-method	BStringViews-class
==,BStringViews,BStringViews-method	BStringViews-class
==,BStringViews,character-method	BStringViews-class
==,character,BString-method	BString-class
==,character,BStringViews-method	BStringViews-class
==,XInteger,XInteger-method	Biostrings-internals
==,XRaw,XRaw-method	Biostrings-internals
AAString	AAString-class
AAString-class	AAString-class
AA_ALPHABET	AAString-class
adjacentViews	BStringViews-constructors
align1	BStringAlign-class
align1,BStringAlign-method	BStringAlign-class
align2	BStringAlign-class
align2,BStringAlign-method	BStringAlign-class
alignScore	needwunsQS
alignScore.needwunsQS	needwunsQS
alphabet	BString-class
alphabet,AAString-method	AAString-class
alphabet,BString-method	BString-class
alphabet,BStringAlign-method	BStringAlign-class
alphabet,BStringCodec-method	Biostrings-internals
alphabet,DNAString-method	DNAString-class
alphabet,RNAString-method	RNAString-class
alphabetFrequency	alphabetFrequency
alphabetFrequency,BString-method	alphabetFrequency
alphabetFrequency,BStringViews-method	alphabetFrequency
alphabetFrequency,DNAString-method	alphabetFrequency
alphabetFrequency,RNAString-method	alphabetFrequency
AMINO_ACID_CODE	AMINO_ACID_CODE
as.character,BString-method	BString-class
as.character,BStringViews-method	BStringViews-class
as.complex,DNAString-method	toComplex
as.integer,XInteger-method	Biostrings-internals
as.integer,XRaw-method	Biostrings-internals
as.list,BStringViews-method	BStringViews-class
as.matrix,BStringViews-method	BStringViews-class
BLOSUM100	scoring_matrices
BLOSUM45	scoring_matrices
BLOSUM50	scoring_matrices
BLOSUM62	scoring_matrices
BLOSUM80	scoring_matrices
BString	BString-class
BString-class	BString-class
BStringAlign	BStringAlign-class
BStringAlign-class	BStringAlign-class
BStringCodec	Biostrings-internals
BStringCodec-class	Biostrings-internals
BStringPartialMatches-class	BStringPartialMatches-class
BStringViews	BStringViews-constructors
BStringViews,ANY-method	BStringViews-constructors
BStringViews,BString-method	BStringViews-constructors
BStringViews,BStringViews-method	BStringViews-constructors
BStringViews,file-method	BStringViews-constructors
BStringViews-class	BStringViews-class
BStringViews-constructors	BStringViews-constructors
BStringViewsToFASTArecords	BStringViews-io
CharacterToFASTArecords	BStringViews-io
class:AAString	AAString-class
class:BString	BString-class
class:BStringAlign	BStringAlign-class
class:BStringCodec	Biostrings-internals
class:BStringPartialMatches	BStringPartialMatches-class
class:BStringViews	BStringViews-class
class:DNAString	DNAString-class
class:PrintableXRaw	Biostrings-internals
class:RNAString	RNAString-class
class:XInteger	Biostrings-internals
class:XRaw	Biostrings-internals
complement	reverseComplement
complement,BStringViews-method	reverseComplement
complement,DNAString-method	reverseComplement
consmat	align-utils
consmat,BStringViews-method	align-utils
consmat,character-method	align-utils
consmat,list-method	align-utils
consmat,matrix-method	align-utils
countPattern	matchPattern
countPattern,BString-method	matchPattern
countPattern,BStringViews-method	matchPattern
countPattern,character-method	matchPattern
debug_shiftor	Biostrings-internals
debug_utils	Biostrings-internals
debug_XRaw	Biostrings-internals
desc	BStringViews-class
desc,BStringViews-method	BStringViews-class
desc<-	BStringViews-class
desc<-,BStringViews-method	BStringViews-class
DNAString	DNAString-class
DNAString-class	DNAString-class
DNA_ALPHABET	DNAString-class
end	BStringViews-class
end,BStringViews-method	BStringViews-class
FASTArecordsToBStringViews	BStringViews-io
FASTArecordsToCharacter	BStringViews-io
findPalindromes	findPalindromes
findPalindromes,BString-method	findPalindromes
findPalindromes,BStringViews-method	findPalindromes
first	BStringViews-class
first,BStringViews-method	BStringViews-class
GENETIC_CODE	GENETIC_CODE
gregexpr2	gregexpr2
initialize,AAString-method	AAString-class
initialize,BString-method	BString-class
initialize,BStringAlign-method	BStringAlign-class
initialize,BStringCodec-method	Biostrings-internals
initialize,DNAString-method	DNAString-class
initialize,RNAString-method	RNAString-class
initialize,XInteger-method	Biostrings-internals
initialize,XRaw-method	Biostrings-internals
IUPAC_CODE_MAP	IUPAC_CODE_MAP
last	BStringViews-class
last,BStringViews-method	BStringViews-class
lcprefix	pmatchPattern
lcprefix,BString,BString-method	pmatchPattern
lcprefix,BString,character-method	pmatchPattern
lcprefix,character,BString-method	pmatchPattern
lcprefix,character,character-method	pmatchPattern
lcsubstr	pmatchPattern
lcsubstr,BString,BString-method	pmatchPattern
lcsubstr,BString,character-method	pmatchPattern
lcsubstr,character,BString-method	pmatchPattern
lcsubstr,character,character-method	pmatchPattern
lcsuffix	pmatchPattern
lcsuffix,BString,BString-method	pmatchPattern
lcsuffix,BString,character-method	pmatchPattern
lcsuffix,character,BString-method	pmatchPattern
lcsuffix,character,character-method	pmatchPattern
length,BString-method	BString-class
length,BStringAlign-method	BStringAlign-class
length,BStringViews-method	BStringViews-class
length,XInteger-method	Biostrings-internals
length,XRaw-method	Biostrings-internals
letter	letter
letter,BString-method	letter
letter,BStringViews-method	letter
letter,character-method	letter
mask	mask
mask,BString-method	mask
mask,BStringViews-method	mask
mask,character-method	mask
matchDNAPattern	matchPattern
matchLRPatterns	matchLRPatterns
matchLRPatterns,BString-method	matchLRPatterns
matchPattern	matchPattern
matchPattern,BString-method	matchPattern
matchPattern,BStringViews-method	matchPattern
matchPattern,character-method	matchPattern
matchProbePair	matchProbePair
matchProbePair,DNAString-method	matchProbePair
mismatch	matchPattern
mismatch,BStringViews-method	matchPattern
nchar,BString-method	BString-class
nchar,BStringAlign-method	BStringAlign-class
nchar,BStringViews-method	BStringViews-class
needwunsQS	needwunsQS
needwunsQS,BString,BString-method	needwunsQS
needwunsQS,BString,character-method	needwunsQS
needwunsQS,character,BString-method	needwunsQS
needwunsQS,character,character-method	needwunsQS
palindromeArmLength	findPalindromes
palindromeArmLength,BString-method	findPalindromes
palindromeArmLength,BStringViews-method	findPalindromes
palindromeLeftArm	findPalindromes
palindromeLeftArm,BString-method	findPalindromes
palindromeLeftArm,BStringViews-method	findPalindromes
palindromeRightArm	findPalindromes
palindromeRightArm,BString-method	findPalindromes
palindromeRightArm,BStringViews-method	findPalindromes
PAM120	scoring_matrices
PAM250	scoring_matrices
PAM30	scoring_matrices
PAM40	scoring_matrices
PAM70	scoring_matrices
pattern	BStringPartialMatches-class
pattern,BStringPartialMatches-method	BStringPartialMatches-class
pmatchPattern	pmatchPattern
pmatchPattern,BString-method	pmatchPattern
pmatchPattern,BStringViews-method	pmatchPattern
pmatchPattern,character-method	pmatchPattern
print.needwunsQS	needwunsQS
PrintableXRaw	Biostrings-internals
PrintableXRaw-class	Biostrings-internals
read.BStringViews	BStringViews-io
readFASTA	readFASTA
reverse	reverseComplement
reverse,BString-method	reverseComplement
reverse,BStringViews-method	reverseComplement
reverseComplement	reverseComplement
reverseComplement,BStringViews-method	reverseComplement
reverseComplement,DNAString-method	reverseComplement
RNAString	RNAString-class
RNAString-class	RNAString-class
RNA_ALPHABET	RNAString-class
score	BStringAlign-class
score,BStringAlign-method	BStringAlign-class
scoring.matrices	scoring_matrices
show,BString-method	BString-class
show,BStringAlign-method	BStringAlign-class
show,BStringPartialMatches-method	BStringPartialMatches-class
show,BStringViews-method	BStringViews-class
show,externalptr-method	Biostrings-internals
show,PrintableXRaw-method	Biostrings-internals
show,XInteger-method	Biostrings-internals
show,XRaw-method	Biostrings-internals
start	BStringViews-class
start,BStringViews-method	BStringViews-class
subBString	subBString
subject	BStringViews-class
subject,BStringViews-method	BStringViews-class
subpatterns	BStringPartialMatches-class
subpatterns,BStringPartialMatches-method	BStringPartialMatches-class
substr	subBString
substr,BString-method	subBString
substr,BStringViews-method	subBString
substring	subBString
substring,BString-method	subBString
substring,BStringViews-method	subBString
subviews	subBString
toComplex	toComplex
toComplex,DNAString-method	toComplex
toString,BString-method	BString-class
toString,BStringViews-method	BStringViews-class
toString,XRaw-method	Biostrings-internals
views	BStringViews-constructors
width	BStringViews-class
width,BStringViews-method	BStringViews-class
write.BStringViews	BStringViews-io
writeFASTA	readFASTA
XInteger	Biostrings-internals
XInteger-class	Biostrings-internals
XRaw	Biostrings-internals
XRaw-class	Biostrings-internals
yeastSEQCHR1	yeastSEQCHR1
[,BString-method	BString-class
[,BStringPartialMatches-method	BStringPartialMatches-class
[,BStringViews-method	BStringViews-class
[,PrintableXRaw-method	Biostrings-internals
[,XInteger-method	Biostrings-internals
[,XRaw-method	Biostrings-internals
[<-,BString-method	BString-class
[<-,BStringViews-method	BStringViews-class
[<-,XInteger-method	Biostrings-internals
[<-,XRaw-method	Biostrings-internals
[[,BStringViews-method	BStringViews-class
[[<-,BStringViews-method	BStringViews-class
