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. |
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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, 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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