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

J 2013

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

HON, Jiří, Tomáš MARTÍNEK, Kamil RAJDL a Matej LEXA

Základní údaje

Originální název

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

Autoři

HON, Jiří (203 Česká republika), Tomáš MARTÍNEK (203 Česká republika, garant), Kamil RAJDL (203 Česká republika, domácí) a Matej LEXA (703 Slovensko, domácí)

Vydání

Bioinformatics, Oxford, Oxford University Press, 2013, 1367-4803

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.621

Kód RIV

RIV/00216224:14330/13:00068371

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.1093/bioinformatics/btt299

UT WoS

000322337000012

Klíčová slova anglicky

H-DNA; R/Bioconductor; pattern matching; dynamic programming; triplex; searching; annotation

Změněno: 13. 3. 2018 14:21, doc. Ing. Matej Lexa, Ph.D.

Anotace

V originále

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).

Návaznosti

LG13010, projekt VaV

Název: Zastoupení ČR v European Research Consortium for Informatics and Mathematics (Akronym: ERCIM-CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Zastoupení ČR v European Research Consortium for Informatics and Mathematics

Citovat

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. Bioinformatics. Oxford: Oxford University Press, 2013, roč. 29, č. 15, s. 1900-1901. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btt299.

@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, 2013, roč.~29, č.~15, s.~1900-1901. ISSN~1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btt299.

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