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

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

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.

Original languageEnglish
Title of host publicationProceedings of the 2019 IEEE 26th International Conference on Electronics, Electrical Engineering and Computing, INTERCON 2019
PublisherInstitute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)9781728136462
DOIs
StatePublished - Aug 2019
Event26th IEEE International Conference on Electronics, Electrical Engineering and Computing, INTERCON 2019 - Lima, Peru
Duration: 12 Aug 201914 Aug 2019

Publication series

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

Conference

Conference26th IEEE International Conference on Electronics, Electrical Engineering and Computing, INTERCON 2019
Country/TerritoryPeru
CityLima
Period12/08/1914/08/19

Bibliographical note

Funding Information:
This research was supported by the National University of San Agustin (UNSA).

Publisher Copyright:
© 2019 IEEE.

Keywords

  • Alignment
  • BLAST
  • DNA
  • GPU
  • Optimization

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