Work

Efficient Parallel Implementations of Multiple Sequence Alignment using BSP/CGM Model

Year: 2014

Type: conference-paper

Abstract: Multiple sequence alignment is a fundamental tool in bioinformatics, widely used for predicting protein structure and function, reconstructing phylogeny and several other biological sequence analyses. Because it is a NP-hard problem, several studies have been conducted to propose efficient methods to solve it. Based on the well-known approximate algorithm proposed by Gusfield [8], we present two parallel solutions for this problem using the BSP/CGM model, with MPI and CUDA implementations. The results show that the use of parallel processing allows the manipulation of more and larger sequences.

Source: International Workshop on Programming Models and Applications for Multicores and Manycores (PMAM)

DOI: 10.1145/2560683.2560698

Authors: Jucele F. A. Vasconcellos, Christiane Nishibe, Nalvo F. Almeida, Edson N. Cáceres

Institution: Universidade Federal de Mato Grosso do Sul

Language: English

Topic: Parallel Computing and Optimization Techniques

Subfield: Hardware and Architecture

Field: Computer Science

Domain: Physical Sciences

Open Access status: bronze

Funders: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Conselho Nacional de Desenvolvimento Científico e Tecnológico

OpenAlex ID: W2079682109

FWCI: 0.188

Cites: 32

Cited by: 1

Related to: 10