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@article{1107853,
author = {Hon, Jiří and Martínek, Tomáš and Rajdl, Kamil and Lexa, Matej},
article_location = {Oxford},
article_number = {15},
doi = {http://dx.doi.org/10.1093/bioinformatics/btt299},
keywords = {H-DNA; R/Bioconductor; pattern matching; dynamic programming; triplex; searching; annotation},
language = {eng},
issn = {1367-4803},
journal = {Bioinformatics},
title = {Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences},
url = {http://bioinformatics.oxfordjournals.org/content/29/15/1900.abstract.html},
volume = {29},
year = {2013}
}
TY - JOUR
ID - 1107853
AU - Hon, Jiří - Martínek, Tomáš - Rajdl, Kamil - Lexa, Matej
PY - 2013
TI - Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences
JF - Bioinformatics
VL - 29
IS - 15
SP - 1900-1901
EP - 1900-1901
PB - Oxford University Press
SN - 13674803
KW - H-DNA
KW - R/Bioconductor
KW - pattern matching
KW - dynamic programming
KW - triplex
KW - searching
KW - annotation
UR - http://bioinformatics.oxfordjournals.org/content/29/15/1900.abstract.html
L2 - http://bioinformatics.oxfordjournals.org/content/29/15/1900.abstract.html
N2 - Upgrade and integration of triplex software into the R/Bioconductor framework. 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 2-D and 3-D 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. R package triplex is available from Bioconductor (bioconductor.org).
ER -
HON, Jiří, Tomáš MARTÍNEK, Kamil RAJDL a Matej LEXA. Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences. \textit{Bioinformatics}. Oxford: Oxford University Press, roč.~29, č.~15, s.~1900-1901. ISSN~1367-4803. doi:10.1093/bioinformatics/btt299. 2013.
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