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Parallel protein multiple sequence alignment approaches: a systematic literature review.
- Source :
-
Journal of Supercomputing . Feb2023, Vol. 79 Issue 2, p1201-1234. 34p. - Publication Year :
- 2023
-
Abstract
- Multiple sequence alignment approaches refer to algorithmic solutions for the alignment of biological sequences. Since multiple sequence alignment has exponential time complexity when a dynamic programming approach is applied, a substantial number of parallel computing approaches have been implemented in the last two decades to improve their performance. In this paper, we present a systematic literature review of parallel computing approaches applied to multiple sequence alignment algorithms for proteins, published in the open literature from 1988 to 2022; we extracted articles from four scientific databases: ACM Digital Library, IEEE Xplore, Science Direct and SpringerLink, and four journals: Bioinformatics, PLOS Computational Biology, PLOS ONE, and Scientific Reports. Additionally, in order to cover other potential databases and journals, we performed a transversal search through Google Scholar. We conducted a selection process that yielded 106 research articles; then, we analyzed these articles and defined a classification framework. Additionally, we point out some directions and trends for parallel computing approaches for multiple sequence alignment, as well as some unsolved problems. [ABSTRACT FROM AUTHOR]
- Subjects :
- *SEQUENCE alignment
*AMINO acid sequence
*SCIENCE databases
*COMPUTATIONAL biology
Subjects
Details
- Language :
- English
- ISSN :
- 09208542
- Volume :
- 79
- Issue :
- 2
- Database :
- Academic Search Index
- Journal :
- Journal of Supercomputing
- Publication Type :
- Academic Journal
- Accession number :
- 161306401
- Full Text :
- https://doi.org/10.1007/s11227-022-04697-9