Journal article

HON Jiří, MARTÍNEK Tomáš, RAJDL Kamil and LEXA Matej. Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences. Bioinformatics. Oxford: Oxford University Press, 2013, vol. 29, no. 15, pp. 1900-1901. ISSN 1367-4803.
Publication language:english
Original title:Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences
Title (cs):Triplex: balíček prostředí R/Bioconductor pro identifikaci a vizualizaci potenciálních intramolekulárních triplexů v DNA sekvencích
Pages:1900-1901
Place:GB
Year:2013
Journal:Bioinformatics, Vol. 29, No. 15, Oxford, GB
ISSN:1367-4803
Keywords
triplex; H-DNA; R; Bioconductor; gene regulation; pattern search;  visualization
Annotation
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{
   author = {Ji{\v{r}}{\'{i}} Hon and Tom{\'{a}}{\v{s}} Mart{\'{i}}nek
	and Kamil Rajdl and Matej Lexa},
   title = {Triplex: an R/Bioconductor package for identification and
	visualization of potential intramolecular triplex patterns
	in DNA sequences},
   pages = {1900--1901},
   journal = {Bioinformatics},
   volume = {29},
   number = {15},
   year = {2013},
   ISSN = {1367-4803},
   language = {english},
   url = {http://www.fit.vutbr.cz/research/view_pub.php?id=10445}
}

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