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

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About: Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences Goto Sponge NotDistinct Permalink

An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	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. 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. (en)
Title	Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences (en)
skos:prefLabel	Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences (en)
skos:notation	RIV/00216305:26230/13:PU106424!RIV14-MSM-26230___
http://linked.open...avai/riv/aktivita	P S Z
http://linked.open...avai/riv/aktivity	P(ED1.1.00/02.0070), P(LG13010), S, Z(MSM0021630528)
http://linked.open...iv/cisloPeriodika	15
http://linked.open...vai/riv/dodaniDat	2014
http://linked.open...aciTvurceVysledku	Hon, Jiří Martínek, Tomáš
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Vysoké učení technické v Brně / Fakulta informačních technologií
http://linked.open...dnocenehoVysledku	111903
http://linked.open...ai/riv/idVysledku	RIV/00216305:26230/13:PU106424
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	triplex, H-DNA, R, Bioconductor, gene regulation, pattern search, visualization (en)
http://linked.open.../riv/klicoveSlovo	visualization Bioconductor H-DNA gene regulation pattern search triplex R
http://linked.open...odStatuVydavatele	GB - Spojené království Velké Británie a Severního Irska
http://linked.open...ontrolniKodProRIV	[6BBB1B17C393]
http://linked.open...i/riv/nazevZdroje	BIOINFORMATICS
http://linked.open...in/vavai/riv/obor	IN
http://linked.open...ichTvurcuVysledku	2 (xsd:int)
http://linked.open...cetTvurcuVysledku	4 (xsd:int)
http://linked.open...vavai/riv/projekt	Czech Republic representation in the European Research Consortium for Informatics and Mathematics (ERCIM) IT4Innovations Centre of Excellence
http://linked.open...UplatneniVysledku	2013
http://linked.open...v/svazekPeriodika	29
http://linked.open...iv/tvurceVysledku	Lexa, Matej Martínek, Tomáš Hon, Jiří Rajdl, Kamil
http://linked.open...ain/vavai/riv/wos	000322337000012
http://linked.open...n/vavai/riv/zamer	Výzkum informačních technologií z hlediska bezpečnosti
issn	1367-4803
number of pages	2 (xsd:int)
http://bibframe.org/vocab/doi	10.1093/bioinformatics/btt299
http://localhost/t...ganizacniJednotka	26230

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