Result Details

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

HON, J.; MARTÍNEK, T.; RAJDL, K.; LEXA, M. Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences. BIOINFORMATICS, 2013, vol. 29, no. 15, p. 1900-1901. ISSN: 1367-4803.
Type
journal article
Language
English
Authors
Hon Jiří, Ing., Ph.D.
Martínek Tomáš, doc. Ing., Ph.D., DCSY (FIT)
Rajdl Kamil, Mgr.
Lexa Matej, Ing., Ph.D., DCSY (FIT)
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.

Keywords

triplex; H-DNA; R; Bioconductor; gene regulation; pattern search;  visualization

Published
2013
Pages
1900–1901
Journal
BIOINFORMATICS, vol. 29, no. 15, ISSN 1367-4803
DOI
10.1093/bioinformatics/btt299
UT WoS
000322337000012
BibTeX 
@article{BUT103564,
  author="Jiří {Hon} and Tomáš {Martínek} and Kamil {Rajdl} and Matej {Lexa}",
  title="Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences",
  journal="BIOINFORMATICS",
  year="2013",
  volume="29",
  number="15",
  pages="1900--1901",
  doi="10.1093/bioinformatics/btt299",
  issn="1367-4803"
}
Projects
Advanced secured, reliable and adaptive IT, BUT, Vnitřní projekty VUT, FIT-S-11-1, start: 2011-01-01, end: 2013-12-31, completed
Centrum excelence IT4Innovations, MŠMT, Operační program Výzkum a vývoj pro inovace, ED1.1.00/02.0070, start: 2011-01-01, end: 2015-12-31, completed
Security-Oriented Research in Information Technology, MŠMT, Institucionální prostředky SR ČR (např. VZ, VC), MSM0021630528, start: 2007-01-01, end: 2013-12-31, running
Departments
Department of Computer Systems (DCSY)
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