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Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns
Jiří Hon1, Tomáš Martínek, Kamil Rajdl
1Department of Computer Systems, Faculty of Information Technology, Brno Technical University, Božetěchova 2, 61266 Brno, Czech Republic.
Bioinformatics (Oxford, England)
|May 28, 2013
Summary
The R package "triplex" identifies DNA sequences forming H-DNA structures. It integrates seamlessly with Bioconductor tools for genomic analysis and visualization.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Intramolecular triplexes (H-DNA) play roles in gene regulation.
- Efficient identification and visualization of H-DNA forming sequences are needed.
Purpose of the Study:
- To develop an R/Bioconductor package for detecting H-DNA forming sequences.
- To integrate H-DNA analysis within the existing bioinformatics framework.
Main Methods:
- Combined a triplex DNA search algorithm with visualization tools.
- Developed the R/Bioconductor package 'triplex'.
- Utilized Biostrings and GRanges classes for data integration.
Main Results:
- The 'triplex' package enables searching DNA sequences for H-DNA forming patterns.
- Provides 2D and 3D visualizations of identified triplexes.
- Results are integrated with Bioconductor for downstream analysis with packages like Gviz.
Conclusions:
- The 'triplex' package offers a versatile tool for H-DNA analysis in R/Bioconductor.
- Facilitates the study of H-DNA in genomic data.
- Enhances visualization and integration capabilities for H-DNA research.
