Tag: Discriminative Motif

DECOD 1.0.1 – Fast and Accurate Discriminative Motif Finding

DECOD 1.0.1

:: DESCRIPTION

DECOD (DECOnvolved Discriminative) is a tool for finding discriminative DNA motifs, i.e. motifs that are over-represented in one set of sequences but are depleted from another.

::DEVELOPER

DECOD team

:: SCREENSHOTS

DECOD

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 DECOD

:: MORE INFORMATION

Citation

DECOD: fast and accurate discriminative DNA motif finding.
Huggins P, Zhong S, Shiff I, Beckerman R, Laptenko O, Prives C, Schulz MH, Simon I, Bar-Joseph Z.
Bioinformatics. 2011 Sep 1;27(17):2361-7. doi: 10.1093/bioinformatics/btr412.

Discriminative HMMs – Find Discriminative Motif to Predict Protein Subcellular Localization

Discriminative HMMs

:: DESCRIPTION

Discriminative HMMs (Hidden Markov models) predicts localizations using motifs that are present in a compartment but absent in other, nearby, compartments by utilizing an hierarchical structure that mimics the protein sorting mechanism.

::DEVELOPER

Tien-ho Lin, Robert F. Murphy, and Ziv Bar-Joseph

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Discriminative HMMs

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2011 Mar-Apr;8(2):441-51.
Discriminative motif finding for predicting protein subcellular localization.
Lin TH, Murphy RF, Bar-Joseph Z.

DiMO 1.6 / DAMO- Discriminative Motif Optimizer

DiMO 1.6 / DAMO

:: DESCRIPTION

DiMO is discriminative motif optimizer.

DAMO (Discriminative Additive Model Optimization)is a Python implementation of the Discriminative Motif Optimizer (DiMO) program and extends it to include adjacent di-nucleotide interactions.

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R
  • Python

:: DOWNLOAD

 DiMO, DAMO

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 1;30(7):941-8. doi: 10.1093/bioinformatics/btt748. Epub 2013 Dec 24.
Discriminative motif optimization based on perceptron training.
Patel RY1, Stormo GD.

BMC Bioinformatics. 2018 Mar 6;19(1):86. doi: 10.1186/s12859-018-2104-7.
Comparison of discriminative motif optimization using matrix and DNA shape-based models.
Ruan S, Stormo GD