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Strategies for Multiple Sequence Alignment [PDF]
BioTechniques, 2002 We present an overview of multiple sequence alignments to outline the practical consequences for the choices among different techniques and parameters. We begin with a discussion of the scoring methods for quantifying the quality of a multiple sequence ...
Hugh B. Nicholas +2 more
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OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy [PDF]
BMC Bioinformatics, 2003 Background The alignment of two or more protein sequences provides a powerful guide in the prediction of the protein structure and in identifying key functional residues, however, the utility of any prediction is completely dependent on the accuracy of ...
Searle Stephen MJ +4 more
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Pairwise Heuristic Sequence Alignment Algorithm Based on Deep Reinforcement Learning
IEEE Open Journal of Engineering in Medicine and Biology, 2021 Goal: Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used method for comparative analysis of biological genomes.
Yong-Joon Song +4 more
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Frontiers in Genetics, 2021 As a key algorithm in bioinformatics, sequence alignment algorithm is widely used in sequence similarity analysis and genome sequence database search.
Haipeng Shi +3 more
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Developments in Algorithms for Sequence Alignment: A Review
Biomolecules, 2022 The continuous development of sequencing technologies has enabled researchers to obtain large amounts of biological sequence data, and this has resulted in increasing demands for software that can perform sequence alignment fast and accurately.
Jiannan Chao, Furong Tang, Lei Xu
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EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment
Algorithms for Molecular Biology, 2023 Background Adding sequences into an existing (possibly user-provided) alignment has multiple applications, including updating a large alignment with new data, adding sequences into a constraint alignment constructed using biological knowledge, or ...
Chengze Shen +3 more
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NGlyAlign: an automated library building tool to align highly divergent HIV envelope sequences
BMC Bioinformatics, 2021 Background The high variability in envelope regions of some viruses such as HIV allow the virus to establish infection and to escape subsequent immune surveillance. This variability, as well as increasing incorporation of N-linked glycosylation sites, is
Elma H. Akand, John M. Murray
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Explaining human mobility predictions through a pattern matching algorithm
EPJ Data Science, 2022 Understanding what impacts the predictability of human movement is a key element for the further improvement of mobility prediction models. Up to this day, such analyses have been conducted using the upper bound of predictability of human mobility ...
Kamil Smolak +2 more
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A benchmark study of sequence alignment methods for protein clustering
BMC Bioinformatics, 2018 Background Protein sequence alignment analyses have become a crucial step for many bioinformatics studies during the past decades. Multiple sequence alignment (MSA) and pair-wise sequence alignment (PSA) are two major approaches in sequence alignment ...
Yingying Wang, Hongyan Wu, Yunpeng Cai
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Spark-based Parallelization of Basic Local Alignment Search Tool [PDF]
International Journal Bioautomation, 2020 Sequence alignment is a key link of bioinformatics analysis. The basic local alignment search tool (BLAST) is a popular sequence alignment algorithm with high accuracy. However, the BLAST is inefficient in comparing and analyzing a massive amount of gene
Hui Wang +4 more
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