Supplementary Website for DECOD: Fast and Accurate Discriminative Motif Finding

• Summary

  DECOD 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.

  DECOD is written in Java and therefore can be run on multiple platforms. It has an easy-to-use GUI interface, and it can also be run in command line mode for batch processing.

• Original paper

  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. (* Equal contributors)

• Software download

  Latest release: DECOD V1.01 (2011.10.24)     Readme

• Supplementary results for the p53 dataset:

  1. Top 10 motifs recovered by DECOD for each comparison and matching with known motifs using STAMP:
     • WT p53 vs 6KR p53
       
     • 6KR p53 vs 6KQ p53
       
     • 6KQ p53 vs Control
       
     
     
  2. Top 10 motifs recovered by DME2 for each comparison and matching with known motifs using STAMP:
     • WT p53 vs 6KR p53
       
     • 6KR p53 vs 6KQ p53
       
     • 6KQ p53 vs Control
       
     
     
  3. Top 10 motifs recovered by CMF for each comparison and matching with known motifs using STAMP:
     • WT p53 vs 6KR p53
       
     • 6KR p53 vs 6KQ p53
       
     • 6KQ p53 vs Control
       

• Support

  Please contact Shan Zhong at szhong {at} andrew.cmu.edu for bug report or technical support.