Description Details Author(s) References See Also Examples
This package provides functions for the identification and visualization of potential intramolecular triplex (H-DNA) patterns in DNA sequences.
This package is essentially an R interface to the underlying C
implementation of a dynamic-programming search startegy of the same name
(Lexa et al., 2011). The main functionality of the original program was to detect
the positions of subsequences in a much larger sequence capable of folding
into an intramolecular triplex (H-DNA) made of as many cannonical nucleotide
triplets as possible (see
triplex.search). In creating its
incarnation in R, we extended this
basic functionality, to include the calculation of exact base-pairing in the
triple helices, which allowed us to extend the functionality of the package
towards visualization showing the exact base-pairing in 1D, 2D or 3D (see
Matej Lexa, Tomas Martinek, Kamil Rajdl, Jiri Hon
Maintainer: Jiri Hon <email@example.com>
Lexa, M., Martinek, T., Burgetova, I., Kopecek, D., Brazdova, M.: A dynamic programming algorithm for identification of triplex-forming sequences, In: Bioinformatics, Vol. 27, No. 18, 2011, Oxford, GB, p. 2510-2517, ISSN 1367-4803
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seq <- DNAString("GGAAAGCAATGCCAGGCAGGG") t <- triplex.search(seq, min_score=10, p_value=1) triplex.diagram(t) ## Not run: triplex.3D(t) ## End(Not run) triplex.score.table() triplex.group.table()
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