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

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Authors

HON Jiří MARTÍNEK Tomáš RAJDL Kamil LEXA Matej

Year of publication 2013
Type Article in Periodical
Magazine / Source Bioinformatics
MU Faculty or unit

Faculty of Informatics

Citation
Web http://bioinformatics.oxfordjournals.org/content/29/15/1900.abstract.html
Doi http://dx.doi.org/10.1093/bioinformatics/btt299
Field Informatics
Keywords H-DNA; R/Bioconductor; pattern matching; dynamic programming; triplex; searching; annotation
Description Upgrade and integration of triplex software into the R/Bioconductor framework. 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 2-D and 3-D 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. R package triplex is available from Bioconductor (bioconductor.org).
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