triplex: Search and visualize intramolecular triplex-forming sequences in DNA

This package provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many cannonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.

AuthorJiri Hon, Matej Lexa, Tomas Martinek and Kamil Rajdl with contributions from Daniel Kopecek
Date of publicationNone
MaintainerJiri Hon <jiri.hon@gmail.com>
LicenseBSD_2_clause + file LICENSE
Version1.14.0
http://www.fi.muni.cz/~lexa/triplex/

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Files in this package

triplex/DESCRIPTION
triplex/LICENSE
triplex/NAMESPACE
triplex/NEWS
triplex/R
triplex/R/TriplexViews-class.R triplex/R/constants.R triplex/R/triplex.3D.R triplex/R/triplex.align.R triplex/R/triplex.diagram.R triplex/R/triplex.input.R triplex/R/triplex.search.R triplex/R/triplex.table.R
triplex/build
triplex/build/vignette.rds
triplex/inst
triplex/inst/CITATION
triplex/inst/doc
triplex/inst/doc/triplex.R
triplex/inst/doc/triplex.Rnw
triplex/inst/doc/triplex.pdf
triplex/man
triplex/man/TriplexViews-class.Rd
triplex/man/figures
triplex/man/figures/triplex.pdf
triplex/man/figures/triplex.png
triplex/man/figures/triplex2d.png
triplex/man/figures/triplex3d.png
triplex/man/figures/types.pdf
triplex/man/figures/types.png
triplex/man/ins.Rd triplex/man/lend.Rd triplex/man/lstart.Rd triplex/man/lwidth.Rd triplex/man/pvalue.Rd triplex/man/triplex-package.Rd triplex/man/triplex.3D.Rd triplex/man/triplex.alignment.Rd triplex/man/triplex.diagram.Rd triplex/man/triplex.group.table.Rd triplex/man/triplex.score.table.Rd triplex/man/triplex.search.Rd
triplex/src
triplex/src/Biostrings_stubs.c
triplex/src/IRanges_stubs.c
triplex/src/R_init_triplex.c
triplex/src/XVector_stubs.c
triplex/src/align.c
triplex/src/align.h
triplex/src/align_interface.c
triplex/src/align_interface.h
triplex/src/dl_list.c
triplex/src/dl_list.h
triplex/src/interval.c
triplex/src/interval.h
triplex/src/libtriplex.c
triplex/src/libtriplex.h
triplex/src/progress.c
triplex/src/progress.h
triplex/src/search.c
triplex/src/search.h
triplex/src/search_interface.c
triplex/src/search_interface.h
triplex/vignettes
triplex/vignettes/fig
triplex/vignettes/fig/triplex.pdf
triplex/vignettes/fig/triplex3d.png
triplex/vignettes/fig/triplex3d2.png
triplex/vignettes/fig/types.pdf
triplex/vignettes/triplex.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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