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Bioinformatics. 2013 Aug 1;29(15):1900-1. doi: 10.1093/bioinformatics/btt299. Epub 2013 May 24.

Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences.

Author information

1
Department of Computer Systems, Faculty of Information Technology, Brno Technical University, Božetěchova 2, 61266 Brno, Czech Republic.

Abstract

MOTIVATION:

Upgrade and integration of triplex software into the R/Bioconductor framework.

RESULTS:

We combined a previously published implementation of a triplex DNA search algorithm with visualization to create a versatile R/Bioconductor package 'triplex'. The new package provides functions that can be used to search Bioconductor genomes and other DNA sequence data for occurrence of nucleotide patterns capable of forming intramolecular triplexes (H-DNA). Functions producing 2D and 3D diagrams of the identified triplexes allow instant visualization of the search results. Leveraging the power of Biostrings and GRanges classes, the results get fully integrated into the existing Bioconductor framework, allowing their passage to other Genome visualization and annotation packages, such as GenomeGraphs, rtracklayer or Gviz.

AVAILABILITY:

R package 'triplex' is available from Bioconductor (bioconductor.org).

CONTACT:

lexa@fi.muni.cz

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
23709494
DOI:
10.1093/bioinformatics/btt299
[Indexed for MEDLINE]

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