GibbsModule

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Reference:

    Dan Xie, Jun Cai, Na-Yu Chia, Huck H. Ng and Sheng Zhong. Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells. Genome Research. 18:1325-1335.

Downloads:

    Datasets (please refer to the paper for the descriptions of the datasets) :
    Simulation data 1 (positions of inserted motifs)       Simulation data 2 (positions of inserted motifs)       Simulation data 3 (positions of inserted motifs)
    Muscle enhancer data
    Oct4-Sox2-Nanog data(2k)      Oct4-Sox2-Nanog data(3k)      Oct4-Sox2-Nanog data(4k)      Oct4-Sox2-Nanog data(5k)
    Klf data
   
    Software:
    GibbsModule : Linux version
    GibbsModule_mac : MacOS version
    Source Code : Source code of GibbsModule

User Manual:

    Usage : ./GibbsModule -i Inputfile -l Motif_length -o Species_num -t Iteration [-a matching score] [-b mismatch penalty] [-c open indel penalty] [-d extending penalty]
    Parameters:
    -i Inputfile: path\filename of input file
    -l Motif_length: expectation of motif length
    -o Species_num: number of orthologs
    -t Iteration: number of iterations for the program to converge
    [matching score: matching score for module alingment (default: 1)]
    [mismatch penalty: mismatch penalty for module alingment (default: 0.33)]
    [open indel penalty: open indel penalty for module alingment (default: 1)]
    [extending penalty: extending penalty for module alingment (default: 0.33)]

    A detailed and comprehensive user manual is ready for download in pdf format: User Manual for GibbsModule




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