Abstract

ARIAS-LOPEZ, Mauricio  and  VELASCO-MEDINA, Jaime. Hardware implementation of modified Needleman-Wunsch algorithm using a parallel architecture. Rev. ing. biomed. [online]. 2018, vol.12, n.23, pp.53-62. ISSN 1909-9762.  https://doi.org/10.24050/19099762.n23.2018.1163.

This paper proposes a DNA sequence pair global alignment processor design. The processor main functional block is a two-dimensional parallel array that allows simultaneous computations, reducing the processing time compared to the software implementation. In this work, the designed hardware performs over 400 nucleotides sequence alignment corresponding to the Mus musculus transition protein 1 (Tnp1), mRNA and the Rattus norvegicus transition protein 1 (Tnp1), mRNA. The implemented algorithm is k-band, a Needleman-Wunsch global alignment algorithm modification, where calculations are made only on the matrix diagonals, establishing a band that can be of a variable size. Simulations of the proposed design are performed using K = 2, 4, 6, 8 and 10 bands.

Keywords : Needleman-Wunsch Algorithm; Global Alignment; Parallel Array; DNA Sequences.

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