AminoAcidAlphabet-class
                        Class "NucleotideAlphabet" represents
                        alphabets used in DNA or RNA
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
LongestCommonPrefix-class
                        Class of longest common prefix lengths for
                        suffix array elemets
NucleotideAlphabet-class
                        Class "NucleotideAlphabet" represents
                        alphabets used in DNA or RNA
NucleotideString        Functions to convert a character string to a
                        BioString object
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
anySameLetter           Generic to find the strings which contain a
                        particular letter
gapletter<-             function to modify the gap letter in an
                        alphabet
matchDNAPattern         Generic to find all matches of a pattern in a
                        DNA string
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
