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pwalign

Perform pairwise sequence alignments


Bioconductor version: Release (3.19)

The two main functions in the package are pairwiseAlignment() and stringDist(). The former solves (Needleman-Wunsch) global alignment, (Smith-Waterman) local alignment, and (ends-free) overlap alignment problems. The latter computes the Levenshtein edit distance or pairwise alignment score matrix for a set of strings.

Author: Patrick Aboyoun [aut], Robert Gentleman [aut], Hervé Pagès [cre]

Maintainer: Hervé Pagès <hpages.on.github at gmail.com>

Citation (from within R, enter citation("pwalign")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("pwalign")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("pwalign")
Pairwise Sequence Alignments PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, Genetics, SequenceMatching, Sequencing, Software
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License Artistic-2.0
Depends BiocGenerics, S4Vectors, IRanges, Biostrings(>= 2.71.5)
Imports methods, utils
System Requirements
URL https://bioconductor.org/packages/pwalign
Bug Reports https://github.com/Bioconductor/pwalign/issues
See More
Suggests RUnit
Linking To S4Vectors, IRanges, XVector, Biostrings
Enhances Rmpi
Depends On Me amplican, hiReadsProcessor, iPAC, MethTargetedNGS, QSutils, R453Plus1Toolbox, sangeranalyseR, sangerseqR, CleanBSequences
Imports Me ChIPpeakAnno, ClustIRR, CNEr, crisprShiny, DominoEffect, enhancerHomologSearch, girafe, GUIDEseq, HTSeqGenie, IMMAN, IsoformSwitchAnalyzeR, LinTInd, methylscaper, motifbreakR, MSA2dist, openPrimeR, QuartPAC, Rcpi, scanMiR, ShortRead, SPLINTER, StructuralVariantAnnotation, svaNUMT, TFBSTools, XNAString
Suggests Me Biostrings, idpr, msa, RSVSim, dowser, seqtrie
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package pwalign_1.0.0.tar.gz
Windows Binary pwalign_1.0.0.zip
macOS Binary (x86_64) pwalign_1.0.0.tgz
macOS Binary (arm64) pwalign_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/pwalign
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pwalign
Bioc Package Browser https://code.bioconductor.org/browse/pwalign/
Package Short Url https://bioconductor.org/packages/pwalign/
Package Downloads Report Download Stats