Learn R Programming

Biostrings (version 2.40.2)

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.

Copy Link

Version

Version

2.40.2

License

Artistic-2.0

Maintainer

Last Published

February 15th, 2017

Functions in Biostrings (2.40.2)

Known HNF4alpha binding sequences

An annotation data file for CHR1 in the yeastSEQ package

lowlevel-matching

Low-level matching functions

AMINO_ACID_CODE

The Single-Letter Amino Acid Code

letterFrequency

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

PairwiseAlignments-io

Write a PairwiseAlignments object to a file

reverseComplement

Sequence reversing and complementing

BOC_SubjectString-class

BOC\_SubjectString and BOC2\_SubjectString objects

Matching a dictionary of patterns against a reference

Read/write an XStringSet object from/to a file

dinucleotideFrequencyTest

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

A replacement for R standard gregexpr function

Percent Sequence Identity

matchPDict-inexact

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

DNAString-class

DNAString objects

Find "theoretical amplicons" mapped to a probe pair

MultipleAlignment-class

MultipleAlignment objects

pairwiseAlignment

Optimal Pairwise Alignment

XStringSetList-class

XStringSetList objects

Longest Common Prefix/Suffix/Substring searching functions

Subsetting a string

findPalindromes

Searching a sequence for palindromes

MaskedXString-class

MaskedXString objects

RNAString-class

RNAString objects

XStringPartialMatches-class

XStringPartialMatches objects

Translating letters of a sequence

XStringQuality-class

PhredQuality, SolexaQuality and IlluminaQuality objects

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

Injecting a hard mask in a sequence

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

Pad and clip strings

Masking by content (or by position)

Versions of bacteriophage phiX174 complete genome and sample short reads

Trim Flanking Patterns from Sequences

(Deprecated) Needleman-Wunsch Global Alignment

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

Translating DNA/RNA sequences

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

matchLRPatterns

Find paired matches in a sequence

String searching functions

Some miscellaneous stuff

Biostrings internals

Biostrings internals

AAString objects

AlignedXStringSet-class

AlignedXStringSet and QualityAlignedXStringSet objects

The IUPAC Extended Genetic Alphabet

Show (display) detailed object content

Utility functions related to sequence alignment

The Standard Genetic Code and its known variants

longestConsecutive

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

replaceLetterAt

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

substitution.matrices

Scoring matrices

PairwiseAlignments-class

PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects

XStringSet-comparison

Comparing and ordering the elements in one or more XStringSet objects

XStringViews-class

The XStringViews class

PWM creating, matching, and related utilities

String Distance/Alignment Score Matrix

nucleotideFrequency

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

QualityScaledXStringSet-class

QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects

Turning a DNA sequence into a vector of complex numbers

BString objects

XStringSet-class

XStringSet objects