三重体：一个用于鉴定和可视化 DNA 序列中潜在的分子内三重体模式的 R/Bioconductor 包。
Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences.
机构信息
Department of Computer Systems, Faculty of Information Technology, Brno Technical University, Božetěchova 2, 61266 Brno, Czech Republic.
出版信息
Bioinformatics. 2013 Aug 1;29(15):1900-1. doi: 10.1093/bioinformatics/btt299. Epub 2013 May 24.
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.
AVAILABILITY
R package 'triplex' is available from Bioconductor (bioconductor.org).
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
将三联软件升级并集成到 R/Bioconductor 框架中。
结果
我们将先前发布的三联 DNA 搜索算法的实现与可视化相结合，创建了一个功能强大的 R/Bioconductor 包“triplex”。新的软件包提供了可以用于在 Bioconductor 基因组和其他 DNA 序列数据中搜索能够形成分子内三联体（H-DNA）的核苷酸模式的功能。生成所识别的三联体的 2D 和 3D 图的功能允许即时可视化搜索结果。利用 Biostrings 和 GRanges 类的强大功能，结果完全集成到现有的 Bioconductor 框架中，允许它们传递到其他基因组可视化和注释包，如 GenomeGraphs、rtracklayer 或 Gviz。
可用性
R 包“triplex”可从 Bioconductor（bioconductor.org）获得。
联系人
补充信息
补充数据可在 Bioinformatics 在线获得。
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