Metaheuristics for multiple sequence alignment: A systematic review

A Comprehensive Review of Bio-Inspired Optimization Algorithms Including Applications in Microelectronics and Nanophotonics

The application of artificial intelligence in everyday life is becoming all-pervasive and unavoidable. Within that vast field, a special place belongs to biomimetic/bio-inspired algorithms for multiparameter optimization, which find their use in a large number of areas. Novel methods and advances are being published at an accelerated pace. Because of that, in spite of the fact that there are a lot of surveys and reviews in the field, they quickly become dated. Thus, it is of importance to keep pace with the current developments. In this review, we first consider a possible classification of bio-inspired multiparameter optimization methods because papers dedicated to that area are relatively scarce and often contradictory. We proceed by describing in some detail some more prominent approaches, as well as those most recently published. Finally, we consider the use of biomimetic algorithms in two related wide fields, namely microelectronics (including circuit design optimization) and nanophotonics (including inverse design of structures such as photonic crystals, nanoplasmonic configurations and metamaterials). We attempted to keep this broad survey self-contained so it can be of use not only to scholars in the related fields, but also to all those interested in the latest developments in this attractive area.

Recent Advances in β-Glucosidase Sequence and Structure Engineering: A Brief Review

β-glucosidases (BGLs) play a crucial role in the degradation of lignocellulosic biomass as well as in industrial applications such as pharmaceuticals, foods, and flavors. However, the application of BGLs has been largely hindered by issues such as low enzyme activity, product inhibition, low stability, etc. Many approaches have been developed to engineer BGLs to improve these enzymatic characteristics to facilitate industrial production. In this article, we review the recent advances in BGL engineering in the field, including the efforts from our laboratory. We summarize and discuss the BGL engineering studies according to the targeted functions as well as the specific strategies used for BGL engineering.

A survey on the algorithm and development of multiple sequence alignment

Multiple sequence alignment (MSA) is an essential cornerstone in bioinformatics, which can reveal the potential information in biological sequences, such as function, evolution and structure. MSA is widely used in many bioinformatics scenarios, such as phylogenetic analysis, protein analysis and genomic analysis. However, MSA faces new challenges with the gradual increase in sequence scale and the increasing demand for alignment accuracy. Therefore, developing an efficient and accurate strategy for MSA has become one of the research hotspots in bioinformatics. In this work, we mainly summarize the algorithms for MSA and its applications in bioinformatics. To provide a structured and clear perspective, we systematically introduce MSA's knowledge, including background, database, metric and benchmark. Besides, we list the most common applications of MSA in the field of bioinformatics, including database searching, phylogenetic analysis, genomic analysis, metagenomic analysis and protein analysis. Furthermore, we categorize and analyze classical and state-of-the-art algorithms, divided into progressive alignment, iterative algorithm, heuristics, machine learning and divide-and-conquer. Moreover, we also discuss the challenges and opportunities of MSA in bioinformatics. Our work provides a comprehensive survey of MSA applications and their relevant algorithms. It could bring valuable insights for researchers to contribute their knowledge to MSA and relevant studies.