Entry: AAString-class
Aliases: class:AAString AAString-class AA_ALPHABET initialize,AAString-method AAString alphabet,AAString-method
Keywords: methods classes
Description: The AAString class
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: BString-class
Aliases: class:BString BString-class initialize,BString-method BString show,BString-method length,BString-method nchar,BString-method [,BString-method [<-,BString-method ==,BString,BString-method ==,BString,character-method ==,character,BString-method !=,BString,BString-method !=,BString,character-method !=,character,BString-method as.character,BString-method toString,BString-method alphabet alphabet,BString-method
Keywords: methods classes
Description: The BString class
URL: ../../../library/Biostrings/html/BString-class.html

Entry: BStringAlign-class
Aliases: class:BStringAlign BStringAlign-class BStringAlign initialize,BStringAlign-method align1 align1,BStringAlign-method align2 align2,BStringAlign-method score score,BStringAlign-method length,BStringAlign-method nchar,BStringAlign-method alphabet,BStringAlign-method show,BStringAlign-method
Keywords: methods classes
Description: The BStringAlign class
URL: ../../../library/Biostrings/html/BStringAlign-class.html

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

Entry: BStringViews-class
Aliases: class:BStringViews BStringViews-class subject subject,BStringViews-method length,BStringViews-method start start,BStringViews-method first first,BStringViews-method end end,BStringViews-method last last,BStringViews-method width width,BStringViews-method nchar,BStringViews-method desc desc,BStringViews-method desc<- desc<-,BStringViews-method show,BStringViews-method [,BStringViews-method [<-,BStringViews-method [[,BStringViews-method [[<-,BStringViews-method ==,BStringViews,BStringViews-method ==,BStringViews,BString-method ==,BStringViews,character-method ==,BString,BStringViews-method ==,character,BStringViews-method !=,BStringViews,BStringViews-method !=,BStringViews,BString-method !=,BStringViews,character-method !=,BString,BStringViews-method !=,character,BStringViews-method as.character,BStringViews-method as.matrix,BStringViews-method as.list,BStringViews-method toString,BStringViews-method
Keywords: methods classes
Description: The BStringViews class
URL: ../../../library/Biostrings/html/BStringViews-class.html

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

Entry: BStringViews-io
Aliases: read.BStringViews write.BStringViews FASTArecordsToCharacter CharacterToFASTArecords FASTArecordsToBStringViews BStringViewsToFASTArecords
Keywords: manip
Description: Input/output of BStringViews objects
URL: ../../../library/Biostrings/html/BStringViews-io.html

Entry: Biostrings internals
Aliases: debug_XRaw debug_shiftor debug_utils show,externalptr-method class:XRaw XRaw-class XRaw length,XRaw-method as.integer,XRaw-method toString,XRaw-method initialize,XRaw-method show,XRaw-method ==,XRaw,XRaw-method !=,XRaw,XRaw-method [,XRaw-method [<-,XRaw-method class:PrintableXRaw PrintableXRaw-class PrintableXRaw show,PrintableXRaw-method [,PrintableXRaw-method class:XInteger XInteger-class XInteger length,XInteger-method as.integer,XInteger-method initialize,XInteger-method show,XInteger-method ==,XInteger,XInteger-method !=,XInteger,XInteger-method [,XInteger-method [<-,XInteger-method class:BStringCodec BStringCodec-class BStringCodec initialize,BStringCodec-method alphabet,BStringCodec-method
Keywords: internal methods classes
Description: Biostrings internals
URL: ../../../library/Biostrings/html/Biostrings-internals.html

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

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

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

Entry: align-utils
Aliases: consmat consmat,matrix-method consmat,character-method consmat,list-method consmat,BStringViews-method
Keywords: methods
Description: Utility functions related to sequence alignment
URL: ../../../library/Biostrings/html/align-utils.html

Entry: alphabetFrequency
Aliases: alphabetFrequency alphabetFrequency,BString-method alphabetFrequency,DNAString-method alphabetFrequency,RNAString-method alphabetFrequency,BStringViews-method
Keywords: category
Description: Function to calculate the frequency of letters in a biological sequence
URL: ../../../library/Biostrings/html/alphabetFrequency.html

Entry: findPalindromes
Aliases: findPalindromes findPalindromes,BString-method findPalindromes,BStringViews-method palindromeArmLength palindromeArmLength,BString-method palindromeArmLength,BStringViews-method palindromeLeftArm palindromeLeftArm,BString-method palindromeLeftArm,BStringViews-method palindromeRightArm palindromeRightArm,BString-method palindromeRightArm,BStringViews-method
Keywords: methods
Description: Searching a sequence for 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: letter
Aliases: letter letter,character-method letter,BString-method letter,BStringViews-method
Keywords: methods
Description: Subsetting a string
URL: ../../../library/Biostrings/html/letter.html

Entry: mask
Aliases: mask mask,BString-method mask,character-method mask,BStringViews-method
Keywords: methods
Description: Masking portions of a sequence
URL: ../../../library/Biostrings/html/mask.html

Entry: matchLRPatterns
Aliases: matchLRPatterns matchLRPatterns,BString-method
Keywords: methods
Description: Find patterns defined by a left and a right part in a sequence
URL: ../../../library/Biostrings/html/matchLRPatterns.html

Entry: matchPattern
Aliases: matchPattern matchPattern,character-method matchPattern,BString-method matchPattern,BStringViews-method countPattern countPattern,character-method countPattern,BString-method countPattern,BStringViews-method mismatch mismatch,BStringViews-method matchDNAPattern
Keywords: methods
Description: String searching functions
URL: ../../../library/Biostrings/html/matchPattern.html

Entry: matchProbePair
Aliases: matchProbePair matchProbePair,DNAString-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,BString-method needwunsQS,BString,character-method needwunsQS,BString,BString-method print.needwunsQS alignScore.needwunsQS alignScore
Keywords: models methods
Description: quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm
URL: ../../../library/Biostrings/html/needwunsQS.html

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

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

Entry: reverseComplement
Aliases: reverse reverse,BString-method reverse,BStringViews-method complement complement,DNAString-method complement,BStringViews-method reverseComplement reverseComplement,DNAString-method reverseComplement,BStringViews-method
Keywords: methods manip
Description: Sequence reversing and complementing
URL: ../../../library/Biostrings/html/reverseComplement.html

Entry: scoring.matrices
Aliases: scoring.matrices BLOSUM45 BLOSUM50 BLOSUM62 BLOSUM80 BLOSUM100 PAM30 PAM40 PAM70 PAM120 PAM250
Keywords: utilities data datasets
Description: Scoring matrices
URL: ../../../library/Biostrings/html/scoring_matrices.html

Entry: subBString
Aliases: subBString subviews substr substr,BString-method substr,BStringViews-method substring substring,BString-method substring,BStringViews-method
Keywords: methods manip
Description: Fast substring extraction
URL: ../../../library/Biostrings/html/subBString.html

Entry: toComplex
Aliases: toComplex toComplex,DNAString-method as.complex,DNAString-method
Keywords: methods
Description: Converting a DNAString to a vector of complexes
URL: ../../../library/Biostrings/html/toComplex.html

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