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  • 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