BIORED - A Genetic Algorithm for Pattern Detection in Biosequences

• Type: Article in International Conference Proceedings Book
• Date: 2009

Authors

Pedro Pereira (Author) Other; Fernando Silva (Author) FCUP; Nuno A Fonseca (Author) Other

Conference proceedings International

Title: ADVANCES IN SOFT COMPUTING

Pages: 156-165

2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 08)

Salamanca, SPAIN, OCT 22-24, 2008

Indexing

ISI Web of Knowledge - 2 Citations

Scopus - 2 Citations

Scientific classification

FOS: Natural sciences > Mathematics

Other information

Authenticus ID: P-003-SZN

DOI: 10.1007/978-3-540-85861-4_19

Abstract (EN): 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/bi-ored/. An online demo is available at the same address.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 10