Base 5 vs. Karp-Rabin as optimizations in the BLAST heuristic for the alignment of DNA sequences

Franklin L.A. Cruz-Gamero, Cesar A. Beltran-Castanon, Juan Carlos Gutierrez Caceres

Resultado de la investigación: Capítulo del libro/informe/acta de congresoContribución a la conferenciarevisión exhaustiva

Resumen

In bioinformatics, the database of biological sequences increases at a dizzying rate, with the alignment algorithms used for the comparison of sequences determining genetic distances, generation of phylogenetic trees, etc. This work seeks to compare the incorporation of the Rabin-Karp and Base 5 algorithms as possible optimizations during the generation of seed indexes of the BLAST alignment algorithm to align multiple query sequences with the DNA sequence of the human genome as sequence of reference. The tests were processed sequentially and using GPU in the MANATI supercomputer of the High Performance Computational Center of the Peruvian Amazon of the IIAP, showing a better performance for a possible optimization of BLAST in the generation of hash keys with the algorithm taken from Base 5 for long sequences (genomes) with short keys, generating maximum dispersion. However, for short sequences or longer keys, it is advisable to use Karp-Rabin, reducing this dispersion.

Idioma originalInglés
Título de la publicación alojadaProceedings of the 2019 IEEE 26th International Conference on Electronics, Electrical Engineering and Computing, INTERCON 2019
EditorialInstitute of Electrical and Electronics Engineers Inc.
ISBN (versión digital)9781728136462
DOI
EstadoPublicada - ago. 2019
Evento26th IEEE International Conference on Electronics, Electrical Engineering and Computing, INTERCON 2019 - Lima, Perú
Duración: 12 ago. 201914 ago. 2019

Serie de la publicación

NombreProceedings of the 2019 IEEE 26th International Conference on Electronics, Electrical Engineering and Computing, INTERCON 2019

Conferencia

Conferencia26th IEEE International Conference on Electronics, Electrical Engineering and Computing, INTERCON 2019
País/TerritorioPerú
CiudadLima
Período12/08/1914/08/19

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Publisher Copyright:
© 2019 IEEE.

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