Detail publikace

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

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

Jazyk

en

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.

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",
  annote="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.",
  address="NEUVEDEN",
  chapter="103564",
  doi="10.1093/bioinformatics/btt299",
  edition="NEUVEDEN",
  howpublished="print",
  institution="NEUVEDEN",
  number="15",
  volume="29",
  year="2013",
  month="september",
  pages="1900--1901",
  publisher="NEUVEDEN",
  type="journal article in Web of Science"
}