title: Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  R package 'triplex' is available from Bioconductor (bioconductor.org).
  
  
  BACKGROUND
  lexa@fi.muni.cz
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Computer Systems, Faculty of Information Technology, Brno Technical University, Božetěchova 2, 61266 Brno, Czech Republic.
authors.forename: Jiří
authors.initials: J
authors.lastname: Hon
authors.forename: Tomáš
authors.initials: T
authors.lastname: Martínek
authors.forename: Kamil
authors.initials: K
authors.lastname: Rajdl
authors.forename: Matej
authors.initials: M
authors.lastname: Lexa
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D004247:DNA / Q000737:chemistry*; D023281:Genomics; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: C051802:triplex DNA; D004247:DNA