Software

• SCREEN, Factorbook and other tools as part of the ENCODE Consortium:

  • SCREEN (github): Search Candidate cis-Regulatory Elements by ENCODE.
  • Factorbook: A wiki-based collections of transcription factors with ENCODE ChIP-seq data.
  • LogoJS (github): a Javascript package for creating sequence logos and embedding them in web applications
    
    

• Protein-protein interactions:

  • Docking Benchmark: A large set of test cases for evaluating the performance of docking algorithms
  • ZDOCK: Rigid-body protein-protein docking software, using a fast Fourier transform based search algorithm
  • ZDOCK Conv3D: ZDOCK optimized with a new convolution library, resulting in improved speed and less memory usage
  • ZDOCK Server: An automated server for running ZDOCK, with capabilities for blocking and filtering contact residues
  • RDOCK: A refinement method to minimize energy and re-rank ZDOCK predictions
  • ATLAS: The ATLAS database is a manually curated repository containing the binding affinities for TCRs and their antigens
    
    

• Transposon movement in genomic DNA:

  • TEMP2 (github): An algorithm for detecting transposable element movement
  • TEMP: The older version of TEMP2
    
    

• Analysis of deep sequencing data on small RNA pathways:

  • piPipes: A small RNA analysis pipeline 
    
    

• Transcription factor binding:

  • Possum: Simple matrix-based motif search
  • CARRIE: Generate transcriptional regulatory networks from microarray and promoter sequence data
  • Cis-element information: Count matrices and background info for some cis-elements
    
    

• Find clusters of transcription factor binding sites in DNA sequences: 

• • Cluster-Buster (Newest method - our favorite!)
  • Comet (Includes statistical significance estimates)
  • Cister (Our original method)
    
    

• Find diagnostic motifs in a set of regulatory (e.g. promoter or enhancer) sequences:

  • GLAM: Gapless local alignment of multiple sequences (motif discovery)
  • Clover: Find overrepresented motifs in DNA sequences
  • ROVER: Find relatively overrepresented motifs in DNA sequences. New Java Version Available
  • REPFIND: Find clustered, exact repeats in nucleotide sequences
  • MotifViz: Integration of tools for detecting overrepresented motifs
  • SeqVISTA: A viewer of sequences and their annotations with a motif module for integrating transcriptional regulation analysis tools
    
    

• Protein Structure:

  • K2: A genetic algorithm-based protein structure alignment tool
  • FAST: A newer protein structure alignment tool, based on graph theory
  • SMM: A matrix-based algorithm for predicting peptides binding to Major Histocompatibility Complex