DNAshapedTFBS specifications

Information


Unique identifier OMICS_28067
Name DNAshapedTFBS
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python, Shell (Bash)
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.0
Stability Stable
Requirements
biopython, python, python2, scikit-learn, shape, pandas, python3, tffm
Maintained Yes

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Versioning


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Documentation


Maintainers


  • person_outline Wyeth Wasserman
  • person_outline Remo Rohs

Publication for DNAshapedTFBS

DNAshapedTFBS citation

library_books

Comparison of discriminative motif optimization using matrix and DNA shape based models

2018
BMC Bioinformatics
PMCID: 5840810
PMID: 29510689
DOI: 10.1186/s12859-018-2104-7

[…] MO_dinuc model.The gap between the training and testing scores is a measure of overfitting for a model, which generally corresponds to the complexity of the model. Specifically, the highly non-linear DNAshapedTFBS-based models, with their ensemble of decision trees, have larger gaps than the PFM and PWM models, which are linear models (Fig. ). In fact, the training and testing scores of the linear […]

DNAshapedTFBS institution(s)
Centre for Molecular Medicine at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo University Hospital, Oslo, Norway; Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA, USA
DNAshapedTFBS funding source(s)
Supported by the Genome Canada Large Scale Applied Research Grant 174CDE, the Child and Family Research Institute, Vancouver, and the British Columbia Children's Hospital Foundation, the Norwegian Research Council, Helse Sor-Ost, and the University of Oslo through the Centre for Molecular Medicine Norway (NCMM), which is a part of the Nordic European Molecular Biology Laboratory partnership for Molecular Medicine, the National Institutes of Health (grants R01GM106056 and U01GM103804) and the Alfred P. Sloan Foundation.

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