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

HON, Jiří, Tomáš MARTÍNEK, Kamil RAJDL and Matej LEXA. Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences. Bioinformatics. Oxford: Oxford University Press, vol. 29, No 15, p. 1900-1901. ISSN 1367-4803. doi:10.1093/bioinformatics/btt299. 2013.

Basic information

• Original name: Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences
• Authors: HON, Jiří (203 Czech Republic), Tomáš MARTÍNEK (203 Czech Republic, guarantor), Kamil RAJDL (203 Czech Republic, belonging to the institution) and Matej LEXA (703 Slovakia, belonging to the institution).
• Edition: Bioinformatics, Oxford, Oxford University Press, 2013, 1367-4803.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10201 Computer sciences, information science, bioinformatics
• Country of publisher: Czech Republic
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Impact factor: Impact factor: 4.621
• RIV identification code: RIV/00216224:14330/13:00068371
• Organization unit: Faculty of Informatics
• Doi: http://dx.doi.org/10.1093/bioinformatics/btt299
• UT WoS: 000322337000012
• Keywords in English: H-DNA; R/Bioconductor; pattern matching; dynamic programming; triplex; searching; annotation

Abstract

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).

Links

• LG13010, research and development project: Name: Zastoupení ČR v European Research Consortium for Informatics and Mathematics (Acronym: ERCIM-CZ)

Investor: Ministry of Education, Youth and Sports of the CR