0 user reviews
0 user reviews
Already have an account? Sign in to review this tool.
No review has been posted.
No open topic.
- Software type:
- Restrictions to use:
- 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:
- DNAshapeR version 1.0
- R version 3.2.2 or later
- 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:
(Chiu et al., 2015) DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding. Bioinformatics.
- Documentation: http://rohslab.cmb.usc.edu/Documents/DNAshapeR_document.pdf
- Remo Rohs <rohs at usc.edu>
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
This work was supported by the NIH (R01GM106056, R01HG003008 in part, and U01GM103804).
Related Shape prediction tools
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,…
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…
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…
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…