Summary
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.
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Pereira, P., Silva, F., Fonseca, N.A. (2009). BIORED - A Genetic Algorithm for Pattern Detection in Biosequences. In: Corchado, J.M., De Paz, J.F., Rocha, M.P., Fernández Riverola, F. (eds) 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008). Advances in Soft Computing, vol 49. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-85861-4_19
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DOI: https://doi.org/10.1007/978-3-540-85861-4_19
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-85860-7
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