Triplex is an R tool to identify and visualize intramolecular triplex patterns in DNA sequences. The Triplex algorithm detects subsequence positions that can fold into an intramolecular triplex (H-DNA) and visualizes the base-pairing in 1-D, 2-D and 3-D.
Molecular interactions, pathways and networks; Nucleic acid structure analysis; Data visualisation; Computational chemistry
Hon J, Martinek T, Rajdl K, Lexa M "Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences." Bioinformatics. 2013 Aug 1;29(15):1900-1. Epub 2013 May 24. https://doi.org/10.1093/bioinformatics/btt299
PMID: 23709494
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21. https://doi.org/10.1038/nmeth.3252
PMID: 25633503
PMCID: PMC4509590
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600
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