AAString-class          The AAString class
AMINO_ACID_CODE         The Single-Letter Amino Acid Code
BString-class           The BString class
BStringAlign-class      The BStringAlign class
BStringPartialMatches-class
                        The BStringPartialMatches class
BStringViews-class      The BStringViews class
BStringViews-constructors
                        Basic functions for creating BStringViews
                        objects
DNAString-class         The DNAString class
GENETIC_CODE            The Standard Genetic Code
IUPAC_CODE_MAP          The IUPAC Extended Genetic Alphabet
RNAString-class         The RNAString class
alphabetFrequency       Function to calculate the frequency of letters
                        in a biological sequence
consmat                 Utility functions related to sequence alignment
findPalindromes         Searching a sequence for palindromes
gregexpr2               A replacement for R standard gregexpr function
letter                  Subsetting a string
mask                    Masking portions of a sequence
matchLRPatterns         Find patterns defined by a left and a right
                        part in a sequence
matchPattern            String searching functions
matchProbePair          Find "theoretical amplicons" mapped to a probe
                        pair
needwunsQS              quadratic-space, simple gap implementation of
                        Needleman-Wunsch global alignment algorithm
pmatchPattern           Longest Common Prefix/Suffix/Substring
                        searching functions
read.BStringViews       Input/output of BStringViews objects
readFASTA               Functions to read/write FASTA formatted files
reverseComplement       Sequence reversing and complementing
scoring.matrices        Scoring matrices
subBString              Fast substring extraction
toComplex               Converting a DNAString to a vector of complexes
yeastSEQCHR1            An annotation data file for CHR1 in the
                        yeastSEQ package
