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Analysis, Programming
Published in Zaven A. Karian, Edward J. Dudewicz, Modern Statistical, Systems, and GPSS Simulation, 2020
Zaven A. Karian, Edward J. Dudewicz
Simulated Annealing Optimization; ARSTI Optimization. Methods for optimizing systems using simulation are not static, but are constantly developing. For example, an exciting new method called “simulated annealing” (see Johnson (1988) for a complete annotated bibliography, computer code, etc.) burst upon the scene in the 1980s. This method attempts to optimize the function f(x1,…, xk) by sequential choice of new (x1,…, xk) vectors. Many methods attempt the same thing, and simulated annealing (which dates from 1983) was perhaps just the “new kid on the block” at that time. However, the simulated annealing method seems very adept at avoiding a common flaw of optimization methods, namely the tendency to become trapped in local optima (versus a global optimum). For this reason, there are well over 300 papers on the method and interest in it is still high. Although the methodology is not yet complete (for example, there seems to be no way to form a confidence statement on optimality yet), readers with an interest in systems with very large k may find it worth exploring. What are called “genetic algorithms” have emerged as a strong competitor (e.g., see Parsons and Johnson (1997), where a review is given along with an application to DNA sequence assembly).
High-Performance and Customizable Bioinformatic and Biomedical Very-Large-Scale-Integration Architectures
Published in Tomasz Wojcicki, Krzysztof Iniewski, VLSI: Circuits for Emerging Applications, 2017
Yao Xin, Benben Liu, Ray C.C. Cheung, Chao Wang
Analysis for bio-sequence such as DNA, RNA, and protein sequence is one of the most promising and challenging tasks [11]. Specifically, it refers to analyze the sequences to reveal the functions, structures, or mutations. This hidden gene information in the nucleotide sequence is in charge of encoding proteins for organs. Such analysis enables us to explore similarities between different species and to discover fatal diseases that oftentimes represent in forms of DNA base mutations. The technique has been widely applied into personalized medicine, biological research, and forensics. Some major types of these analyses consist of (1) DNA/RNA sequence alignment, which is meant to identify similarities between two or multiple sequences or to map short sequences to a reference genome database; (2) biclustering, originally for data mining application, which is an important method to analyze large-scale biological sequence set [12]; (3) sequence assembly, which is to construct the original DNA sequence with small fragments after sequencing process; and (4) phylogenetic analysis of DNA or protein sequences, which is an important method to find the evolutionary history of organisms from bacteria to humans [13].
Production and partial purification by PEG/citrate ATPS of a β-galactosidase from the new promising isolate Cladosporium tenuissimum URM 7803
Published in Preparative Biochemistry & Biotechnology, 2021
Anderson José Paulo, Maria Carolina de Albuquerque Wanderley, Rafael José Vilela de Oliveira, Willie Anderson dos Santos Vieira, Luiz Carlos Alves, Daniela de Araújo Viana Marques, Attilio Converti, Ana Lúcia Figueiredo Porto
The final amplicons were purified with the kit Wizard® SV Gel and PCR Clean-Up System (Promega, Madison, WI, USA). Sequencing was performed by the Laboratory of Molecular Biology and Evolutionary Biology of UFPE, Recife, Brazil. Sequence assembly and editing were performed using the tools called Pregap4 and Gap4, which belong to the Staden package.[36]