The Standard Genetic Code and its known variants
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
Write a PairwiseAlignments object to a file
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
PhredQuality, SolexaQuality and IlluminaQuality objects
Comparing and ordering the elements in one or more XStringSet objects
Read/write an XStringSet object from/to a file
Utility functions related to sequence alignment
Replace letters in a sequence or set of sequences
Pearson's chi-squared Test and G-tests for String Position Dependence
A replacement for R standard gregexpr function
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
Obtain the length of the longest substring containing only 'letter'
Utility functions operating on the matches returned by a high-level matching function
Matching a dictionary of patterns against a reference
PWM creating, matching, and related utilities
Find "theoretical amplicons" mapped to a probe pair
A function to match a query sequence to the sequences of a set of probes.
Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
Versions of bacteriophage phiX174 complete genome and sample short reads
Longest Common Prefix/Suffix/Substring searching functions
Extract/replace arbitrary substrings from/in a string or set of strings.
Replacing letters in a sequence (or set of sequences) at some specified locations
seqinfo() method for DNAStringSet objects
Turning a DNA sequence into a vector of complex numbers
Concatenate sequences contained in XString, XStringSet and/or XStringViews objects
An annotation data file for CHR1 in the yeastSEQ package