The implementation of bit-parallelism for DNA sequence alignment

International Symposium on Bioinformatics, Chemometrics and Metabolomics

生物科学;化学

Setyorini^1,2 ; Kuspriyanto^1,2 ; Widyantoro, D.H.^1,2 ; Pancoro, A.^1,2

School of Electrical and Informatic Engineering, Bandung Institute of Technology, Bandung, Indonesia^1

Schools of Life Science, TB Bandung, Indonesia^2

关键词: Approximate string matching;    Biological sequence alignment;    Bit parallelism;    Computational process;    Computing process;    Construction process;    DNA sequence alignments;    Matching score;   

Others  :  https://iopscience.iop.org/article/10.1088/1742-6596/835/1/012004/pdf
DOI  :  10.1088/1742-6596/835/1/012004

学科分类：生物科学（综合）

来源: IOP

【 摘 要 】

Dynamic Programming (DP) remain the central algorithm of biological sequence alignment. Matching score computation is the most time-consuming process. Bit-parallelism is one of approximate string matching techniques that transform DP matrix cell unit processing into word unit (groups of cell). Bit-parallelism computate the scores column-wise. Adopting from word processing in computer system work, this technique promise reducing time in score computing process in DP matrix. In this paper, we implement bit-parallelism technique for DNA sequence alignment. Our bit-parallelism implementation have less time for score computational process but still need improvement for there construction process.