BIORED - A Genetic Algorithm for Pattern Detection in Biosequences

Pedro Pereira, Fernando Silva and Nuno A. Fonseca

October 2008

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Abstract

We present a new, efficient and scalable tool, named BIORED, for pattern discovery in proteomic and genomic sequences. It uses a genetic algorithm to find interesting patterns in the form of regular expressions, and a new efficient pattern matching procedure to count pattern occurrences. We studied the performance, scalability and usefulness of BIORED using several databases of biosequences. The results show that BIORED was successful in finding previously known patterns, thus an excellent indicator for its potential. BIORED is available for download under the GNU Public License at http://www.dcc.fc.up.pt/biored/. An online demo is available at the same address.

Bibtex

@InProceedings{pereira-iwpacbb08,
   author =    {P. Pereira and F. Silva and N. A. Fonseca},
   title =     {{BIORED - A Genetic Algorithm for Pattern Detection in Biosequences}},
   booktitle = {{Proceedings of the 2nd International Workshop on Practical Applications 
                 of Computational Biology and Bioinformatics (IWPACBB 2008)}},
   pages =     {156--165},
   volume =    {49},
   series =    {Advances in Intelligent and Soft Computing},
   publisher = {Springer},
   editor =    {J. M. Corchado and J. F. De Paz and M. P. Rocha and F. F. Riverola},
   month =     {October},
   year =      {2008},
   address =   {Salamanca, Spain},
   note =      {Published in 2009},
}

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