Function	Description
allSameLetter	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
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
DNAAlphabet	functions to create DNA and RNA alphabets
DNAPatternAlphabet	functions to create DNA and RNA pattern alphabets
DNASuffixArray	function to create a suffix array for a DNA string
gapletter<-	function to modify the gap letter in an alphabet
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
NucleotideAlphabet-class	Class "NucleotideAlphabet" represents alphabets used in DNA or RNA
NucleotideString	Functions to convert a character string to a BioString object
readFASTA	A function to read FASTA formatted files
reverseComplement	Function to reverse a DNA or RNA sequence and complement each base
sortDNAString	function to sort DNA strings
yeastSEQCHR1	An annotation data file for CHR1 in the yeastSEQ package