Detail publikačního výsledku

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.

Originální název

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

Anglický název

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

Druh

Článek WoS

Originální abstrakt

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.

Anglický abstrakt

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.

Klíčová slova

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

Klíčová slova v angličtině

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

Autoři

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

Rok RIV

2014

Vydáno

13.09.2013

ISSN

1367-4803

Periodikum

BIOINFORMATICS

Svazek

29

Číslo

15

Stát

Spojené království Velké Británie a Severního Irska

Strany od

1900

Strany do

1901

Strany počet

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"
}