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Resumen ejecutivo
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In bioinformatics, the database of biological se-quences increases at a dizzying rate, with the alignment al-gorithms used for the comparison of sequences determininggenetic distances, generation of phylogenetic trees, etc. Thiswork seeks to compare the incorporation of the Rabin-Karpand Base 5 algorithms as possible optimizations during thegeneration of seed indexes of the BLAST alignment algorithmto align multiplequerysequences with the DNA sequence of thehuman genome as sequence of reference. The tests were processedsequentially and using GPU in theMANATIsupercomputer ofthe High Performance Computational Center of the PeruvianAmazon of the IIAP, showing a better performance for a possibleoptimization of BLAST in the generation of hash keys with thealgorithm taken from Base 5 for long sequences (genomes) withshort keys, generating maximum dispersion. However, for shortsequences or longer keys, it is advisable to use Karp-Rabin,reducing this dispersion. |
