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* HIGEDA: A hierarchical gene-set genetic based algorithm for finding subtle motifs in biological sequences
  We have developed HIGEDA, an algorithm that uses the hierarchical gene-set genetic algorithm (HGA) with EM to initiate and search for the best parameters for the motif model. In addition, HIGEDA can identify gapped motifs using a Position Weight Matrix (PWM) and Dynamic Programming (DP) to generate an optimal gapped alignment of the motif model with sequences from the dataset. download
  Program source code HIGEDA was implemented in C++ and supported on Linux and MS Windows. This sourcecode can be compiled with either cl compiler for MS-Windows or g++ compiler for Linux.

   cl /EHsc higeda.cpp
   g++ higeda.cpp -o higeda.out

To run the program:
    HIGEDA  -w < motif length > [-gap < max-consicutive_gaps >]
            [-minw < minimumMotifLength >] [-maxw < maximumMotifLength >]
            -i < input_sequence_file >  [-o < result_output_file > ]
            [-type < dna/protein >] [-popsize < genetic_population_size >]
  Online demo This online demo was developed using ajax technique with PHP scripting language and the higeda program in C++.
  Simulated DNA datasets This packet contains the simulated datasets we used in testing HIGEDA and comparison with GEMFA and EM algorithms. The results are shown in table 1 of the manuscript.
  DNA datasets This packet contains CRP, ERE and E2F datasets we used in testing HIGEDA and comparison with GEMFA, GAME, MEME and BioProspector algorithms. The results are shown in table 2 of the manuscript.
  Protein datasets (I) This packet contains datasets of 8 protein families from PFAM that we used in testing HIGEDA and comparison with MEME algorithm. The results are shown in table 3 of the manuscript.
  Protein datasets (II) This packet contains datasets of the two groups; the first one contains ZZ, SWIRM, ZZ+Myb and ZZ+Myb+SWIRM domains, the second one contains Presenilin Type 1 and Signal peptide peptidase families. These datasets was used to check the ability of HIGEDA in discovering new motifs. The results are shown in table 4 and 5.
  All datasets This packet contains all above datasets.
Additional datasets This packet contains additional datasets (revised version, 09/10/2009).
  Program update version
(09/10/2009)
This packet contains the update version of HIGEDA program to fix the errors of;
- Getting parameters from program command line.
- Reading multi-line fasta format files.
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  Well-known Algorithms 
program sourcecode:
BioProspector 2004
GAME      GEMFA
GLAM2      MEME
Pratt 2.1
RISOTTO      ExMOTIF