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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("triplex")
AuthorJiri Hon, Matej Lexa, Tomas Martinek and Kamil Rajdl with contributions from Daniel Kopecek
Bioconductor views GeneRegulation SequenceMatching
Date of publicationNone
MaintainerJiri Hon <jiri.hon@gmail.com>
LicenseBSD_2_clause + file LICENSE
Version1.14.0
http://www.fi.muni.cz/~lexa/triplex/

View on Bioconductor

Functions

as.character,TriplexViews-method Man page
class:TriplexViews Man page
ins Man page
ins,TriplexViews-method Man page
lend Man page
lend,TriplexViews-method Man page
lstart Man page
lstart,TriplexViews-method Man page
lwidth Man page
lwidth,TriplexViews-method Man page
pvalue Man page
pvalue,TriplexViews-method Man page
score,TriplexViews-method Man page
show,TriplexViews-method Man page
strand,TriplexViews-method Man page
toString,TriplexViews-method Man page
triplex Man page
triplex.3D Man page
triplex.alignment Man page
triplex.diagram Man page
triplex.group.table Man page
triplex-package Man page
triplex.score.table Man page
triplex.search Man page
TriplexViews Man page
TriplexViews-class Man page
TriplexViews-constructor Man page
type,TriplexViews-method Man page

Files

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

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.