Predicts DNA shape features in an ultra-fast, high-throughput manner from genomic sequencing data. The package takes either nucleotide sequence or genomic coordinates as input and generates various graphical representations for visualization and further analysis. DNAshapeR further encodes DNA sequence and shape features as user-defined combinations of k-mer and DNA shape features. The resulting feature matrices can be readily used as input of various machine learning software packages for further modeling studies.

User report

0 user reviews

0 user reviews

No review has been posted.

DNAshapeR forum

No open topic.

DNAshapeR classification

DNAshapeR specifications

Software type:
Package
Restrictions to use:
None
Output data:
Minor groove width, helix twist, propeller twist and Roll can then be visualized in the form of plots, heat maps or genome browser tracks or used for the assembly of feature vectors of user-defined combinations of k-mer and shape features.
Programming languages:
R
Version:
DNAshapeR version 1.0
Requirements:
R version 3.2.2 or later
Interface:
Command line interface
Input data:
The input data can be either nucleotide sequence(s) in FASTA file format or genomic intervals, provided by the user in BED format or derived from public databases.
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Stability:
Stable

Publications

  • (Chiu et al., 2015) DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding. Bioinformatics.
    PMID: 26668005

DNAshapeR support

Documentation

Maintainer

Credits

Institution(s)

Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA; Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland; Faculty of Science, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland

Funding source(s)

This work was supported by the NIH (R01GM106056, R01HG003008 in part, and U01GM103804).

Related Shape prediction tools

Most Recent Tools

Desktop app
3DNA 3DNA

3DNA

A comprehensive software package for the analysis, reconstruction and…

A comprehensive software package for the analysis, reconstruction and visualization of three-dimensional nucleic acid structures. 3DNA can be applied to parallel and antiparallel double helices,…

Web app
QuadBase QuadBase

QuadBase

Allows multiplexed putative G4 (PG4) motif mining in large number of nucleotide…

Allows multiplexed putative G4 (PG4) motif mining in large number of nucleotide sequences and also enables profiling complete prokaryotic genomes. QuadBase is linked with Ensembl's genomic…

Web app
DNAshape DNAshape

DNAshape

A method and web server for predicting DNA structural features in a…

A method and web server for predicting DNA structural features in a high-throughput (HT) manner for massive sequence data. DNAshape provides the framework for the integration of DNA sequence and…

Desktop app
do_x3dna do_x3dna

do_x3dna

Analyzes the structural fluctuations of DNA or RNA during molecular dynamics…

Analyzes the structural fluctuations of DNA or RNA during molecular dynamics simulations. do_x3dna extends the capability of the 3DNA package to GROMACS MD trajectories and includes new methods to…

16 related tools

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.