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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.

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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

DNAshapeR support

Documentation

Maintainer

Credits

Publications

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

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 Z├╝rich, 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).

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