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 letter letter,BString-method initialize,BString-method BString show,BString-method length,BString-method [,BString-method [<-,BString-method ==,BString,BString-method !=,BString,BString-method ==,BString,ANY-method !=,BString,ANY-method ==,ANY,BString-method !=,ANY,BString-method as.character,BString-method toString,BString-method nchar,BString-method subBString subBString,BString-method
Keywords: methods classes
Description: The BString class
URL: ../../../library/Biostrings/html/BString-class.html

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

Entry: BStringViews-constructors
Aliases: BStringViews-constructors initialize,BStringViews-method views adjacentViews BStringViews BStringViews,file-method BStringViews,BString-method BStringViews,BStringViews-method
Keywords: methods
Description: Constructor-like functions and generics for BStringViews objects
URL: ../../../library/Biostrings/html/BStringViews-constructors.html

Entry: Biostrings internals
Aliases: debug_CharBuffer debug_shiftor debug_utils show,externalptr-method class:CharBuffer CharBuffer-class CharBuffer length,CharBuffer-method toString,CharBuffer-method initialize,CharBuffer-method show,CharBuffer-method ==,CharBuffer,CharBuffer-method !=,CharBuffer,CharBuffer-method [,CharBuffer-method [<-,CharBuffer-method class:PrintableCharBuffer PrintableCharBuffer-class PrintableCharBuffer show,PrintableCharBuffer-method [,PrintableCharBuffer-method class:IntBuffer IntBuffer-class IntBuffer length,IntBuffer-method initialize,IntBuffer-method show,IntBuffer-method ==,IntBuffer,IntBuffer-method !=,IntBuffer,IntBuffer-method [,IntBuffer-method [<-,IntBuffer-method class:BStringCodec BStringCodec-class BStringCodec initialize,BStringCodec-method alphabet 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: alphabetFrequency
Aliases: alphabetFrequency alphabetFrequency,BString-method alphabetFrequency,DNAString-method alphabetFrequency,RNAString-method alphabetFrequency,BStringViews-method alphabetFrequency
Keywords: category
Description: Function to calculate the frequency of letters in a biological sequence
URL: ../../../library/Biostrings/html/alphabetFrequency.html

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

Entry: blosum50
Aliases: blosum50
Keywords: datasets
Description: scoring matrix for codon substitution in protein alignments
URL: ../../../library/Biostrings/html/blosum50.html

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

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

Entry: readFASTA
Aliases: readFASTA
Keywords: manip
Description: A function to read 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: yeastSEQCHR1
Aliases: yeastSEQCHR1
Keywords: datasets
Description: An annotation data file for CHR1 in the yeastSEQ package
URL: ../../../library/Biostrings/html/yeastSEQCHR1.html