Biostrings: Efficient manipulation of biological strings

Package `Biostrings'

October 3, 2021

Title Efficient manipulation of biological strings Description Memory efficient string containers, string matching

algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. biocViews SequenceMatching, Alignment, Sequencing, Genetics, DataImport, DataRepresentation, Infrastructure

URL

BugReports Version 2.61.2 License Artistic-2.0 Encoding UTF-8 Author H. Pag?s, P. Aboyoun, R. Gentleman, and S. DebRoy Maintainer H. Pag?s Depends R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>=

0.27.12), IRanges (>= 2.23.9), XVector (>= 0.29.2), GenomeInfoDb Imports methods, utils, grDevices, graphics, stats, crayon LinkingTo S4Vectors, IRanges, XVector Enhances Rmpi Suggests BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit LazyLoad yes Collate 00datacache.R utils.R IUPAC_CODE_MAP.R AMINO_ACID_CODE.R GENETIC_CODE.R XStringCodec-class.R seqtype.R coloring.R XString-class.R XStringSet-class.R XStringSet-comparison.R XStringViews-class.R MaskedXString-class.R XStringSetList-class.R xscat.R XStringSet-io.R letter.R

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R topics documented:

getSeq.R seqinfo.R letterFrequency.R dinucleotideFrequencyTest.R chartr.R reverseComplement.R translate.R toComplex.R replaceAt.R replaceLetterAt.R injectHardMask.R padAndClip.R strsplit-methods.R misc.R SparseList-class.R MIndex-class.R lowlevel-matching.R match-utils.R matchPattern.R maskMotif.R matchLRPatterns.R trimLRPatterns.R matchProbePair.R matchPWM.R findPalindromes.R PDict-class.R matchPDict.R XStringPartialMatches-class.R XStringQuality-class.R QualityScaledXStringSet.R InDel-class.R AlignedXStringSet-class.R PairwiseAlignments-class.R PairwiseAlignmentsSingleSubject-class.R PairwiseAlignments-io.R align-utils.R pmatchPattern.R pairwiseAlignment.R stringDist.R needwunsQS.R MultipleAlignment.R matchprobes.R zzz.R

git_url

git_branch master

git_last_commit 050d572

git_last_commit_date 2021-08-04

Date/Publication 2021-10-03

R topics documented:

AAString-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 align-utils . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 AlignedXStringSet-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 AMINO_ACID_CODE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 chartr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 detail . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 dinucleotideFrequencyTest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 DNAString-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 findPalindromes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 GENETIC_CODE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 getSeq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 gregexpr2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 HNF4alpha . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 InDel-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 injectHardMask . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 IUPAC_CODE_MAP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 letter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 letterFrequency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 longestConsecutive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 lowlevel-matching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 MaskedXString-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 maskMotif . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 match-utils . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 matchLRPatterns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 matchPattern . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

R topics documented:

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matchPDict . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 matchPDict-inexact . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 matchProbePair . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 matchprobes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 matchPWM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66 MIndex-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 misc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 MultipleAlignment-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 needwunsQS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76 nucleotideFrequency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 padAndClip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82 pairwiseAlignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84 PairwiseAlignments-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87 PairwiseAlignments-io . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91 PDict-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94 phiX174Phage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97 pid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99 pmatchPattern . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100 QualityScaledXStringSet-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 replaceAt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103 replaceLetterAt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 reverseComplement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110 RNAString-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112 seqinfo-methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114 stringDist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115 substitution.matrices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116 toComplex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119 translate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120 trimLRPatterns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124 xscat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126 XString-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127 XStringPartialMatches-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130 XStringQuality-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130 XStringSet-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132 XStringSet-comparison . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138 XStringSet-io . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141 XStringSetList-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148 XStringViews-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150 yeastSEQCHR1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153

Index

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AAString-class

AAString-class

AAString objects

Description An AAString object allows efficient storage and manipulation of a long amino acid sequence.

Usage AAString(x="", start=1, nchar=NA)

## Predefined constants:

AA_ALPHABET

# full Amino Acid alphabet

AA_STANDARD

# first 20 letters only

AA_PROTEINOGENIC # first 22 letters only

Arguments

x start, nchar

A single string. Where to start reading from in x and how many letters to read.

Details

The AAString class is a direct XString subclass (with no additional slot). Therefore all functions and methods described in the XString man page also work with an AAString object (inheritance). Unlike the BString container that allows storage of any single string (based on a single-byte character set) the AAString container can only store a string based on the Amino Acid alphabet (see below).

The Amino Acid alphabet

This alphabet contains all letters from the Single-Letter Amino Acid Code (see ?AMINO_ACID_CODE) plus "*" (the stop letter), "-" (the gap letter), "+" (the hard masking letter), and "." (the not a letter or not available letter). It is stored in the AA_ALPHABET predefined constant (character vector). The alphabet() function returns AA_ALPHABET when applied to an AAString object.

Constructor-like functions and generics

In the code snippet below, x can be a single string (character vector of length 1) or a BString object.

AAString(x="",start=1,nchar=NA): Tries to convert x into an AAString object by reading nchar letters starting at position start in x.

Accessor methods

In the code snippet below, x is an AAString object.

alphabet(x): If x is an AAString object, then return the Amino Acid alphabet (see above). See the corresponding man pages when x is a BString, DNAString or RNAString object.

align-utils

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Author(s) H. Pag?s

See Also AMINO_ACID_CODE, letter, XString-class, alphabetFrequency

Examples

AA_ALPHABET a ................
................

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