Publication result detail

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.

Original Title

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

English Title

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

Type

WoS Article

Original 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.

English 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

Key words in English

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

Authors

HON, J.; MARTÍNEK, T.; RAJDL, K.; LEXA, M.

RIV year

2014

Released

13.09.2013

ISBN

1367-4803

Periodical

BIOINFORMATICS

Volume

29

Number

15

State

United Kingdom of Great Britain and Northern Ireland

Pages from

1900

Pages to

1901

Pages count

2

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"
}