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Biostrings (version 2.34.1)

String objects representing biological sequences, and matching algorithms

Description

Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

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Version

Version

2.34.1

License

Artistic-2.0

Maintainer

H Pages

Last Published

February 15th, 2017

Functions in Biostrings (2.34.1)

Injecting a hard mask in a sequence

The IUPAC Extended Genetic Alphabet

matchPDict-inexact

Inexact matching with matchPDict()/countPDict()/whichPDict()

Find "theoretical amplicons" mapped to a probe pair

PairwiseAlignments-io

Write a PairwiseAlignments object to a file

Some miscellaneous stuff

String Distance/Alignment Score Matrix

substitution.matrices

Scoring matrices

XStringSetList-class

XStringSetList objects

XStringViews-class

The XStringViews class

BOC_SubjectString-class

BOC\_SubjectString and BOC2\_SubjectString objects

Biostrings internals

Biostrings internals

findPalindromes

Searching a sequence for palindromes or complemented palindromes

The Standard Genetic Code and its known variants

A function to match a query sequence to the sequences of a set of probes.

PWM creating, matching, and related utilities

Versions of bacteriophage phiX174 complete genome and sample short reads

Percent Sequence Identity

XStringQuality-class

PhredQuality, SolexaQuality and IlluminaQuality objects

XStringSet-class

XStringSet objects

XStringSet-comparison

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

AAString objects

String searching functions

dinucleotideFrequencyTest

Pearson's chi-squared Test and G-tests for String Position Dependence

DNAString-class

DNAString objects

Utility functions operating on the matches returned by a high-level matching function

Matching a dictionary of patterns against a reference

Known HNF4alpha binding sequences

pairwiseAlignment

Optimal Pairwise Alignment

PairwiseAlignments-class

PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects

XStringPartialMatches-class

XStringPartialMatches objects

BString objects

Show (display) detailed object content

Translating letters of a sequence

Subsetting a string

letterFrequency

Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences

matchLRPatterns

Find paired matches in a sequence

nucleotideFrequency

Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)

Pad and clip strings

Longest Common Prefix/Suffix/Substring searching functions

AlignedXStringSet-class

AlignedXStringSet and QualityAlignedXStringSet objects

AMINO_ACID_CODE

The Single-Letter Amino Acid Code

A replacement for R standard gregexpr function

MaskedXString-class

MaskedXString objects

Masking by content (or by position)

MultipleAlignment-class

MultipleAlignment objects

(Deprecated) Needleman-Wunsch Global Alignment

Extract/replace arbitrary substrings from/in a string or set of strings.

replaceLetterAt

Replacing letters in a sequence (or set of sequences) at some specified locations

Turning a DNA sequence into a vector of complex numbers

longestConsecutive

Obtain the length of the longest substring containing only 'letter'

lowlevel-matching

Low-level matching functions

reverseComplement

Sequence reversing and complementing

RNAString-class

RNAString objects

QualityScaledXStringSet-class

QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects

Trim Flanking Patterns from Sequences

Concatenate sequences contained in XString, XStringSet and/or XStringViews objects

Translating DNA/RNA sequences

An annotation data file for CHR1 in the yeastSEQ package