Entry: AminoAcidAlphabet-class
Aliases: AminoAcidAlphabet-class BioStringNewValues,AminoAcidAlphabet,numeric-method
Keywords: classes
Description: Class "NucleotideAlphabet" represents alphabets used in DNA or RNA
URL: ../../../library/Biostrings/html/AminoAcidAlphabet-class.html

Entry: BioAlphabet-class
Aliases: BioAlphabet-class initialize,BioAlphabet-method gapletter<-,BioAlphabet,character-method
Keywords: classes
Description: Class "BioAlphabet" represents alphabets used in biology
URL: ../../../library/Biostrings/html/BioAlphabet-class.html

Entry: BioPatternAlphabet-class
Aliases: BioPatternAlphabet-class BioStringNewValues,BioPatternAlphabet,numeric-method gapletter<-,BioPatternAlphabet,character-method initialize,BioPatternAlphabet-method
Keywords: classes
Description: Class representing alphabets used in patterns for matching biological sequences
URL: ../../../library/Biostrings/html/BioPatternAlphabet-class.html

Entry: BioString-class
Aliases: BioString-class [,BioString-method [,BioString,ANY,ANY,ANY-method [[,BioString-method allSameLetter,BioString,character-method allSameLetter,BioString,BioString-method anySameLetter,BioString,character-method anySameLetter,BioString,BioString-method as.character,BioString-method as.matrix,BioString-method initialize,BioString-method length,BioString-method matchDNAPattern,BioString,BioString-method nchar,BioString,character-method nchar,BioString,missing-method show,BioString-method substr,BioString-method substring,BioString-method
Keywords: classes
Description: Class "BioString", represents a biological sequence
URL: ../../../library/Biostrings/html/BioString-class.html

Entry: BioStringNewValues
Aliases: BioStringNewValues
Keywords: classes internal
Description: generic to do create an object suitable for the values slot of "BioStrings" class
URL: ../../../library/Biostrings/html/BioStringNewValues.html

Entry: DNAAlphabet
Aliases: DNAAlphabet RNAAlphabet
Keywords: classes
Description: functions to create DNA and RNA alphabets
URL: ../../../library/Biostrings/html/DNAAlphabet.html

Entry: DNAPatternAlphabet
Aliases: DNAPatternAlphabet RNAPatternAlphabet
Keywords: classes
Description: functions to create DNA and RNA pattern alphabets
URL: ../../../library/Biostrings/html/DNAPatternAlphabet.html

Entry: DNASuffixArray
Aliases: DNASuffixArray
Keywords: utilities
Description: function to create a suffix array for a DNA string
URL: ../../../library/Biostrings/html/DNASuffixArray.html

Entry: LongestCommonPrefix-class
Aliases: LongestCommonPrefix-class [,LongestCommonPrefix,matrix,missing,missing-method
Keywords: classes
Description: Class of longest common prefix lengths for suffix array elemets
URL: ../../../library/Biostrings/html/LongestCommonPrefix-class.html

Entry: LongestCommonPrefix
Aliases: LongestCommonPrefix
Keywords: internal
Description: Find the longest common prefixes for a suffix array
URL: ../../../library/Biostrings/html/LongestCommonPrefix.html

Entry: NucleotideAlphabet-class
Aliases: NucleotideAlphabet-class BioStringNewValues,NucleotideAlphabet,numeric-method initialize,NucleotideAlphabet-method
Keywords: classes
Description: Class "NucleotideAlphabet" represents alphabets used in DNA or RNA
URL: ../../../library/Biostrings/html/NucleotideAlphabet-class.html

Entry: NucleotideString
Aliases: NucleotideString DNAString
Keywords: classes
Description: Functions to convert a character string to a BioString object
URL: ../../../library/Biostrings/html/NucleotideString.html

Entry: allSameLetter
Aliases: allSameLetter allSameLetter,character,ANY-method
Keywords: classes methods
Description: Generic to find the strings which are repeats of a single letter
URL: ../../../library/Biostrings/html/allSameLetter.html

Entry: alphabetFrequency
Aliases: alphabetFrequency
Keywords: category
Description: function to calculate the frequency of letters in a biological sequence
URL: ../../../library/Biostrings/html/alphabetFrequency.html

Entry: anySameLetter
Aliases: anySameLetter anySameLetter,character,ANY-method
Keywords: classes methods
Description: Generic to find the strings which contain a particular letter
URL: ../../../library/Biostrings/html/anySameLetter.html

Entry: gapletter<-
Aliases: gapletter<-
Keywords: classes
Description: function to modify the gap letter in an alphabet
URL: ../../../library/Biostrings/html/gapletterReplace.html

Entry: matchDNAPattern
Aliases: matchDNAPattern matchDNAPattern,character,ANY-method matchDNAPattern,ANY,character-method
Keywords: classes
Description: Generic to find all matches of a pattern in a DNA string
URL: ../../../library/Biostrings/html/matchDNAPattern.html

Entry: reverseComplement
Aliases: reverseComplement
Keywords: manip
Description: Function to reverse a DNA or RNA sequence and complement each base
URL: ../../../library/Biostrings/html/reverseComplement.html

Entry: sortDNAString
Aliases: sortDNAString
Keywords: utilities
Description: function to sort DNA strings
URL: ../../../library/Biostrings/html/sortDNAString.html

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