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Search and visualize intramolecular triplex-forming sequences in DNA

Bioconductor version: Release (3.1)

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>

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


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PDF R Script Triplex User Guide
PDF   Reference Manual
Text   NEWS


biocViews GeneRegulation, SequenceMatching, Software
Version 1.8.0
In Bioconductor since BioC 2.12 (R-3.0) (2.5 years)
License BSD_2_clause + file LICENSE
Depends R (>= 2.15.0), S4Vectors(>= 0.5.14), IRanges(>= 1.99.1), XVector(>= 0.7.3), Biostrings(>= 2.33.3)
Imports methods, grid, GenomicRanges
LinkingTo S4Vectors, IRanges, XVector, Biostrings
Suggests rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer, GenomeGraphs
Depends On Me
Imports Me
Suggests Me
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