Faculty of Information Technology, BUT

Publication Details

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

HON Jiří, MARTÍNEK Tomáš, RAJDL Kamil and LEXA Matej. Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences. Bioinformatics, vol. 29, no. 15, pp. 1900-1901. ISSN 1367-4803.
Czech title
Triplex: balíček prostředí R/Bioconductor pro identifikaci a vizualizaci potenciálních intramolekulárních triplexů v DNA sekvencích
Type
journal article
Language
english
Authors
Hon Jiří, Ing. (FIT BUT)
Martínek Tomáš, Ing., Ph.D. (DCSY FIT BUT)
Rajdl Kamil, Mgr. (FI MUNI)
Lexa Matej, Ing., Ph.D. (FI MUNI)
Keywords
triplex; H-DNA; R; Bioconductor; gene regulation; pattern search;  visualization
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.

Published
2013
Pages
1900-1901
Journal
Bioinformatics, vol. 29, no. 15, ISSN 1367-4803
Publisher
Oxford University Press
DOI
BibTeX
@ARTICLE{FITPUB10445,
   author = "Ji\v{r}\'{i} Hon and Tom\'{a}\v{s} Mart\'{i}nek and Kamil Rajdl and Matej Lexa",
   title = "Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences",
   pages = "1900--1901",
   journal = "Bioinformatics",
   volume = 29,
   number = 15,
   year = 2013,
   ISSN = "1367-4803",
   doi = "10.1093/bioinformatics/btt299",
   language = "english",
   url = "https://www.fit.vut.cz/research/publication/10445"
}
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