MIL – Multiple Instance Learning for Protein-DNA Interaction Modeling

MIL

:: DESCRIPTION

MIL(multiple-instance learning) is a novel algorithm, which breaks each DNA sequence into multiple overlapping subsequences and models each subsequence separately, therefore implicitly takes into consideration binding site locations, resulting in both higher accuracy and better interpretability of the models.

::DEVELOPER

Jianhua Ruan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  •  MatLab

:: DOWNLOAD

MIL

:: MORE INFORMATION

Citation

Computational modeling of in vivo and in vitro protein-DNA interactions by multiple instance learning.
Gao Z, Ruan J.
Bioinformatics. 2017 Jul 15;33(14):2097-2105. doi: 10.1093/bioinformatics/btx115.

GEM 2.6 – Study Protein-DNA interaction using ChIP-Seq/ChIP-exo data

GEM 2.6

:: DESCRIPTION

GEM (Genome wide Event finding and Motif discovery) is a software tool to study protein-DNA interaction using ChIP-Seq/ChIP-exo data. GEM resolves ChIP data into explanatory motifs and binding events at unsurpassed spatial resolution by linking binding event discovery and motif discovery with positional priors in the context of a generative model of ChIP data and genome sequence.

:: DEVELOPER

the Gifford Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GEM

:: MORE INFORMATION

Citation:

Yuchun Guo, Georgios Papachristoudis, Robert C Altshuler, Georg K Gerber, Tommi S Jaakkola, David K Gifford & Shaun Mahony,
Discovering homotypic binding events at high spatial resolution.
Bioinformatics. 2010 Dec 15;26(24):3028-34. Epub 2010 Oct 21. PMID: 20966006.

Bind-n-Seq – Analysis of in vitro Protein–DNA Interactions

Bind-n-Seq

:: DESCRIPTION

Bind-n-Seq is a new high-throughput method for analyzing protein–DNA interactions in vitro, with several advantages over current methods.

::DEVELOPER

Korf Lab at the University of California, Davis.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/Linux/ Windows
  • Perl

:: DOWNLOAD

 Bind-n-Seq

:: MORE INFORMATION

Citation

Bind-n-Seq: high-throughput analysis of in vitro protein–DNA interactions using massively parallel sequencing
Artem Zykovich, Ian Korf and David J. Segal
Nucl. Acids Res. (2009) 37 (22): e151.

Prediction of Protein-DNA Interactions based on Alpha Shape Modeling

Prediction of Protein-DNA Interactions based on Alpha Shape Modeling

:: DESCRIPTION

Protein–DNA interaction has significant importance in many biological processes. However, the underlying principle of the molecular recognition process is still largely unknown. As more high-resolution 3D structures of protein–DNA complex are becoming available, the surface characteristics of the complex become an important research topic.

::DEVELOPER

 Hong Yan , Signal Processing Lab at City University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
  • CGAL
  • C++ Compiler

:: DOWNLOAD

  Protein–DNA interaction 

:: MORE INFORMATION

Citation:

Weiqiang Zhou and Hong Yan
A Discriminatory Function for Prediction of Protein-DNA Interactions based on Alpha Shape Modeling
Bioinformatics (2010) 26 (20): 2541-2548.

GPS 1.1 – Study Protein-DNA Interaction using ChIP-Seq data

GPS 1.1

:: DESCRIPTION

GPS (Genome Positioning System) is a software tool to study protein-DNA interaction using ChIP-Seq data. GPS builds a probabilistic mixture model to predict the most likely positions of binding events at single-base resolution.

::DEVELOPER

the Gifford Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java

:: DOWNLOAD

 GPS

:: MORE INFORMATION

Citation

Yuchun Guo, Georgios Papachristoudis, Robert C Altshuler, Georg K Gerber, Tommi S Jaakkola, David K Gifford & Shaun Mahony,
Discovering homotypic binding events at high spatial resolution.
Bioinformatics. 2010 Dec 15;26(24):3028-34. Epub 2010 Oct 21.