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A motif finding tool for a set of intergenic sequences
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A motif finding tool for a set of intergenic sequences

You can also directly use command 'g++ MotifClick.cpp -o MotifClick' to complie the cpp file.


./MotifClick input_file [OPTIONS] > OutputFile

input_file: file containing DNA sequences in FASTA format


-w : motif width(default=10)

-n : maximum number of motifs to find(default=5)

-SSD : upper bound of SSD (sum of squared distance, please select 0<SSD<1, default=0.3)

-b 2 : if examine sites on both of DNA strands(default=1 only forward)

-d : upper bound of graph density(default=100)

-s 0 : if want more degenerate sites (default=1 if want fewer sites)

If  you use the code, please cite the reference:

Zhang et al. MotifClick: prediction of cis-regulatory binding sites via merging cliques BMC Bioinformatics 2011, 12:238 (

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