triplex

Search and visualize intramolecular triplex-forming sequences in DNA

Bioconductor version: Release (2.14)

This package provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many cannonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.

Author: Jiri Hon, Matej Lexa, Tomas Martinek and Kamil Rajdl with contributions from Daniel Kopecek

Maintainer: Jiri Hon <jiri.hon at gmail.com>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("triplex")

To cite this package in a publication, start R and enter:

    citation("triplex")

Documentation

PDF R Script Triplex User Guide
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews GeneRegulation, SequenceMatching, Software
Version 1.4.0
In Bioconductor since BioC 2.12 (R-3.0)
License BSD_2_clause + file LICENSE
Depends R (>= 2.15.0), IRanges(>= 1.21.10), XVector(>= 0.3.2), Biostrings(>= 2.31.3)
Imports methods, grid, GenomicRanges
Suggests rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer, GenomeGraphs
System Requirements
URL http://www.fi.muni.cz/~lexa/triplex/
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source triplex_1.4.0.tar.gz
Windows Binary triplex_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) triplex_1.4.0.tgz
Mac OS X 10.9 (Mavericks)
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