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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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Shouji: A Fast and Efficient Pre-Alignment Filter for Sequence Alignment [PDF]
Bioinform., 2019 Motivation: The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability of existing algorithms and compute infrastructures.
Alkan, Can +4 more
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GSAlign: an efficient sequence alignment tool for intra-species genomes
BMC Genomics, 2020 Background Personal genomics and comparative genomics are becoming more important in clinical practice and genome research. Both fields require sequence alignment to discover sequence conservation and variation.
Hsin-Nan Lin, Wen-Lian Hsu
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HELIOS: High-speed sequence alignment in optics. [PDF]
PLoS Computational Biology, 2022 In response to the imperfections of current sequence alignment methods, originated from the inherent serialism within their corresponding electrical systems, a few optical approaches for biological data comparison have been proposed recently.
Ehsan Maleki +2 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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T2VLAD: Global-Local Sequence Alignment for Text-Video Retrieval [PDF]
Computer Vision and Pattern Recognition, 2021 Text-video retrieval is a challenging task that aims to search relevant video contents based on natural language descriptions. The key to this problem is to measure text-video similarities in a joint embedding space.
Xiaohan Wang, Linchao Zhu, Yi Yang
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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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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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