A Framework for Executing Protein Sequence Alignment in Cloud Computing Services

  • Leonardo Reboucas de Carvalho UnB
  • Alba Cristina Alves Melo UnB
  • Aleteia Araujo UnB

Resumo


Protein sequence alignment is a task of great relevance in Bioinformatics and the Hirschberg algorithm is widely used for this task. This work proposes a framework for executing sequence alignment with the Hirschberg algorithm in different cloud computing services. In experiments, our framework was used to align HIV-1 protease sequences using different instances of AWS EC2 and different configurations of AWS Lambda functions.The results show that, for this application, there is a tradeoff between the expected execution time and the cost, e.g., in most cases AWS Lambda provides the best runtime, however at a higher USD cost. In this context, it is important to have a framework that helps in deciding which approach is most appropriate.

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Publicado
26/10/2021
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CARVALHO, Leonardo Reboucas de; MELO, Alba Cristina Alves; ARAUJO, Aleteia. A Framework for Executing Protein Sequence Alignment in Cloud Computing Services. In: SIMPÓSIO EM SISTEMAS COMPUTACIONAIS DE ALTO DESEMPENHO (WSCAD), 22. , 2021, Belo Horizonte. Anais [...]. Porto Alegre: Sociedade Brasileira de Computação, 2021 . p. 48-59. DOI: https://doi.org/10.5753/wscad.2021.18511.