AAString-class          AAString objects
AMINO_ACID_CODE         The Single-Letter Amino Acid Code
BOC_SubjectString-class
                        BOC\_SubjectString and BOC2\_SubjectString
                        objects
DNAString-class         DNAString objects
GENETIC_CODE            The Standard Genetic Code
IRanges-class           IRanges and NormalIRanges objects
IRanges-utils           IRanges utility functions
IUPAC_CODE_MAP          The IUPAC Extended Genetic Alphabet
MaskCollection-class    MaskCollection objects
MaskedXString-class     MaskedXString objects
PDict-class             PDict objects
RNAString-class         RNAString objects
XString-class           BString objects
XStringAlign-class      XStringAlign objects
XStringPartialMatches-class
                        XStringPartialMatches objects
XStringSet-class        BStringSet, DNAStringSet, RNAStringSet and
                        AAStringSet objects
XStringViews-class      The XStringViews class
XStringViews-constructors
                        Basic functions for creating or modifying
                        XStringViews objects
alphabetFrequency       Functions to calculate the frequency of letters
                        in a biological sequence
chartr                  Translating letters of a sequence
consmat                 Utility functions related to sequence alignment
findPalindromes         Searching a sequence for palindromes or
                        complemented palindromes
gregexpr2               A replacement for R standard gregexpr function
injectHardMask          Injecting a hard mask in a sequence
letter                  Subsetting a string
maskMotif               Masking by content (or by position)
match-utils             Utility functions related to pattern matching
matchLRPatterns         Find patterns defined by a left and a right
                        part in a sequence
matchPDict              Searching a sequence for patterns stored in a
                        dictionary
matchPDict-inexact      Inexact matching with matchPDict()
matchPWM                A simple PWM matching function and related
                        utilities
matchPattern            String searching functions
matchProbePair          Find "theoretical amplicons" mapped to a probe
                        pair
needwunsQS              (Deprecated) Needleman-Wunsch Global Alignment
pairwiseAlignment       Optimal Pairwise Alignment
pmatchPattern           Longest Common Prefix/Suffix/Substring
                        searching functions
read.Mask               Read a mask from a file
read.XStringViews       Read/write an XStringSet or XStringViews object
                        from/to a file
readFASTA               Functions to read/write FASTA formatted files
replaceLetterAtLoc      Replacing letters in a sequence at some
                        specified locations
reverseComplement       Sequence reversing and complementing
subXString              Fast substring extraction
substitution.matrices   Scoring matrices
toComplex               Converting a DNAString to a vector of complexes
yeastSEQCHR1            An annotation data file for CHR1 in the
                        yeastSEQ package
