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| allSameLetter | Generic to find the strings which are repeats of a single letter |
| allSameLetter,BioString,BioString-method | Class "BioString", represents a biological sequence |
| allSameLetter,BioString,character-method | Class "BioString", represents a biological sequence |
| allSameLetter,character,ANY-method | Generic to find the strings which are repeats of a single letter |
| alphabetFrequency | function to calculate the frequency of letters in a biological sequence |
| AminoAcidAlphabet-class | Class "NucleotideAlphabet" represents alphabets used in DNA or RNA |
| anySameLetter | Generic to find the strings which contain a particular letter |
| anySameLetter,BioString,BioString-method | Class "BioString", represents a biological sequence |
| anySameLetter,BioString,character-method | Class "BioString", represents a biological sequence |
| anySameLetter,character,ANY-method | Generic to find the strings which contain a particular letter |
| as.character,BioString-method | Class "BioString", represents a biological sequence |
| as.matrix,BioString-method | Class "BioString", represents a biological sequence |
| BioAlphabet-class | Class "BioAlphabet" represents alphabets used in biology |
| BioPatternAlphabet-class | Class representing alphabets used in patterns for matching biological sequences |
| BioString-class | Class "BioString", represents a biological sequence |
| BioStringNewValues,AminoAcidAlphabet,numeric-method | Class "NucleotideAlphabet" represents alphabets used in DNA or RNA |
| BioStringNewValues,BioPatternAlphabet,numeric-method | Class representing alphabets used in patterns for matching biological sequences |
| BioStringNewValues,NucleotideAlphabet,numeric-method | Class "NucleotideAlphabet" represents alphabets used in DNA or RNA |
| DNAAlphabet | functions to create DNA and RNA alphabets |
| DNAPatternAlphabet | functions to create DNA and RNA pattern alphabets |
| DNAString | Functions to convert a character string to a BioString object |
| DNASuffixArray | function to create a suffix array for a DNA string |
| gapletter<-,BioAlphabet,character-method | Class "BioAlphabet" represents alphabets used in biology |
| gapletter<-,BioPatternAlphabet,character-method | Class representing alphabets used in patterns for matching biological sequences |
| initialize,BioAlphabet-method | Class "BioAlphabet" represents alphabets used in biology |
| initialize,BioPatternAlphabet-method | Class representing alphabets used in patterns for matching biological sequences |
| initialize,BioString-method | Class "BioString", represents a biological sequence |
| initialize,NucleotideAlphabet-method | Class "NucleotideAlphabet" represents alphabets used in DNA or RNA |
| length,BioString-method | Class "BioString", represents a biological sequence |
| LongestCommonPrefix-class | Class of longest common prefix lengths for suffix array elemets |
| matchDNAPattern | Generic to find all matches of a pattern in a DNA string |
| matchDNAPattern,ANY,character-method | Generic to find all matches of a pattern in a DNA string |
| matchDNAPattern,BioString,BioString-method | Class "BioString", represents a biological sequence |
| matchDNAPattern,character,ANY-method | Generic to find all matches of a pattern in a DNA string |
| nchar,BioString,character-method | Class "BioString", represents a biological sequence |
| nchar,BioString,missing-method | Class "BioString", represents a biological sequence |
| NucleotideAlphabet-class | Class "NucleotideAlphabet" represents alphabets used in DNA or RNA |
| NucleotideString | Functions to convert a character string to a BioString object |
| reverseComplement | Function to reverse a DNA or RNA sequence and complement each base |
| RNAAlphabet | functions to create DNA and RNA alphabets |
| RNAPatternAlphabet | functions to create DNA and RNA pattern alphabets |
| show,BioString-method | Class "BioString", represents a biological sequence |
| sortDNAString | function to sort DNA strings |
| substr,BioString-method | Class "BioString", represents a biological sequence |
| substring,BioString-method | Class "BioString", represents a biological sequence |
| yeastSEQCHR1 | An annotation data file for CHR1 in the yeastSEQ package |
| [,BioString,ANY,ANY,ANY-method | Class "BioString", represents a biological sequence |
| [,BioString-method | Class "BioString", represents a biological sequence |
| [,LongestCommonPrefix,matrix,missing,missing-method | Class of longest common prefix lengths for suffix array elemets |
| [[,BioString-method | Class "BioString", represents a biological sequence |