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

Varování

Publikace nespadá pod Pedagogickou fakultu, ale pod Fakultu informatiky. Oficiální stránka publikace je na webu muni.cz.
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HON Jiří MARTÍNEK Tomáš RAJDL Kamil LEXA Matej

Rok publikování 2013
Druh Článek v odborném periodiku
Časopis / Zdroj Bioinformatics
Fakulta / Pracoviště MU

Fakulta informatiky

Citace
www http://bioinformatics.oxfordjournals.org/content/29/15/1900.abstract.html
Doi http://dx.doi.org/10.1093/bioinformatics/btt299
Obor Informatika
Klíčová slova H-DNA; R/Bioconductor; pattern matching; dynamic programming; triplex; searching; annotation
Popis 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).
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