Sequence alignment from the perspective of stochastic optimization: a survey

摘要

DNA and protein are the fundamental biological sequences.DNA is a fundamental molecule that plays a vital role in the processesof life. Proteins synthesized by DNA in a cell are the buildingblocks of every living organism. There is a variety of reasons behindthe alignment of biological sequences. Biological sequence alignmenthelps to discover functional and structural similarity of sequences.Biologists work with these aligned sequences to construct phylogenetictrees, characterize protein families, and predict protein structure.Sequence alignment is an extremely promising field of research that ischaracterized by very high computational complexity. Stochasticoptimization is needed for sequence alignment, as it generatesefficient solutions to the problem. The objective of this study is tosurvey recent trends in stochastic optimization for sequence alignmentas means of a guide for researchers who are interested in the sequencealignment problem.