Multiple sequence alignment using genetic algorithms with multithreading

• Grant number: 13/08289-0
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• Start date: September 01, 2013
• End date: January 31, 2015
• Field of knowledge: Physical Sciences and Mathematics - Computer Science
• Principal Investigator: Carlos Roberto Valêncio
• Grantee: Anderson Rici Amorim
• Host Institution: Instituto de Biociências, Letras e Ciências Exatas (IBILCE). Universidade Estadual Paulista (UNESP). Campus de São José do Rio Preto. São José do Rio Preto , SP, Brazil

Abstract

The solution of genomic problems proposed by biologists has become unfeasible without computational tools, which developed intensively bioinformatics allowing cooperation between computer scientists and biologists. The problems complexity evolution brought the need of refinement of many multiple sequence alignment and pattern recognition techniques, mainly through optmization strategies. Thus, the present work proposes the development of a multiple sequence alignment tool using genetic algorithm with multithreading. Then, besides the efficiency of biological results provided by genetic algorithms, mainly related to mutation parameters refinement and crossing over, the project aims the improvement of the execution time performance, through task partitioning during the alignment process, scheduling their operations among the threads.

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

AMORIM, ANDERSON RICI; NEVES, LEANDRO ALVES; VALENCIA, CARLOS ROBERTO; ROBERTO, GUILHERME FREIRE; DONEGA ZAFALON, GERALDO FRANCISCO. An approach for COFFEE objective function to global DNA multiple sequence alignment. COMPUTATIONAL BIOLOGY AND CHEMISTRY, v. 75, p. 39-44, AUG 2018. (13/08289-0)