Next-generation bioinformatics: using many-core processor architecture to develop a web service for sequence alignment.
BACKGROUND
Bioinformatics algorithms and computing power are the main bottlenecks for analyzing huge amount of data generated by the current technologies, such as the 'next-generation' sequencing methodologies. At the same time, most powerful microprocessors are based on many-core chips, yet most applications cannot exploit such power, requiring parallelized algorithms. As an example of next-generation bioinformatics, we have developed from scratch a new parallelization of the Needleman-Wunsch (NW) sequence alignment algorithm for the 64-core Tile64 microprocessor. The unprecedented performance it offers for a standalone personal computer (PC) is discussed, optimally aligning sequences up to 20 times faster than the non-parallelized version, thus saving valuable time.


BACKGROUND
This algorithm is available as a free web service for the scientific community at http://www.sicuma.uma.es/multicore. The open source code is also available on such site.
Gálvez
Sergio
S
Department Lenguajes y Ciencias de la Computación, Universidad de Málaga 29071 Málaga, Spain. galvez@uma.es
Díaz
David
D
Hernández
Pilar
P
Esteban
Francisco J
FJ
Caballero
Juan A
JA
Dorado
Gabriel
G
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D020407:Internet; D016415:Sequence Alignment / Q000379:methods*