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.

Author
Jiri Hon, Matej Lexa, Tomas Martinek and Kamil Rajdl with contributions from Daniel Kopecek
Date of publication
None
Maintainer
Jiri Hon <jiri.hon@gmail.com>
License
BSD_2_clause + file LICENSE
Version
1.14.0
URLs

View on Bioconductor

Man pages

ins
Insertions accessor
lend
Loop end accessor
lstart
Loop start accessor
lwidth
Loop width accessor
pvalue
P-value accessor
triplex.3D
Triplex visualization, 3D representation
triplex.alignment
Triplex alignment
triplex.diagram
Triplex visualization, diagram representation
triplex.group.table
Get default isogroup tables
triplex-package
Triplex search and visualization package
triplex.score.table
Get default scoring tables
triplex.search
Search intramolecular triplex-forming sequences in DNA
TriplexViews-class
The TriplexViews class

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