AAString-class          AAString objects
AMINO_ACID_CODE         The Single-Letter Amino Acid Code
AlignedXStringSet-class
                        AlignedXStringSet and QualityAlignedXStringSet
                        objects
BOC_SubjectString-class
                        BOC\_SubjectString and BOC2\_SubjectString
                        objects
DNAString-class         DNAString objects
GENETIC_CODE            The Standard Genetic Code
IUPAC_CODE_MAP          The IUPAC Extended Genetic Alphabet
InDel-class             InDel objects
MIndex-class            MIndex objects
MaskedXString-class     MaskedXString objects
PDict-class             PDict objects
PairwiseAlignedFixedSubject-class
                        PairwiseAlignedFixedSubject and
                        PairwiseAlignedFixedSubjectSummary objects
QualityScaledXStringSet-class
                        QualityScaledBStringSet,
                        QualityScaledDNAStringSet,
                        QualityScaledRNAStringSet and
                        QualityScaledAAStringSet objects
RNAString-class         RNAString objects
XString-class           BString objects
XStringPartialMatches-class
                        XStringPartialMatches objects
XStringQuality-class    PhredQuality and SolexaQuality objects
XStringSet-class        BStringSet, DNAStringSet, RNAStringSet and
                        AAStringSet objects
XStringViews-class      The XStringViews class
XStringViews-constructors
                        Basic functions for creating or modifying
                        XStringViews objects
align-utils             Utility functions related to sequence alignment
alphabetFrequency       Function to calculate the frequency of letters
                        in a biological sequence and related functions
chartr                  Translating letters of a sequence
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 paired matches in a sequence
matchPDict              Searching a sequence for patterns stored in a
                        preprocessed dictionary
matchPDict-inexact      Inexact matching with
                        matchPDict()/countPDict()/whichPDict()
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
phiX174Phage            Versions of bacteriophage phiX174 complete
                        genome and sample short reads
pid                     Percent Sequence Identity
pmatchPattern           Longest Common Prefix/Suffix/Substring
                        searching functions
read.XStringViews       Read/write an XStringSet or XStringViews object
                        from/to a file
readFASTA               Functions to read/write FASTA formatted files
replaceLetterAt         Replacing letters in a sequence at some
                        specified locations
reverseComplement       Sequence reversing and complementing
stringDist              String Distance/Alignment Score Matrix
subXString              Fast substring extraction
substitution.matrices   Scoring matrices
toComplex               Turning a DNA sequence into a vector of complex
                        numbers
translate               DNA/RNA transcription and translation
yeastSEQCHR1            An annotation data file for CHR1 in the
                        yeastSEQ package
