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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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Bioinformatics in Rice Research, 2018 Let x = (x1 . . . xm) and y = (y1 . . . yn) be two sequences of tokens, aka. strings. We assume the lengths m,n are known and a pair of tokens can be compared in constant time.
Manoj Kumar Gupta +8 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
semanticscholar +1 more source
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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Constrained sequence alignment [PDF]
Bulletin of Mathematical Biology, 1993 This paper presents a dynamic programming algorithm for aligning two sequences when the alignment is constrained to lie between two arbitrary boundary lines in the dynamic programming matrix. For affine gap penalties, the algorithm requires only O(F) computations time and O(M+N) space, when F is the area of the feasible region and M and N are the ...
Chao, Kun-Mao +2 more
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Multiple sequence alignments [PDF]
Current Opinion in Structural Biology, 2005 Multiple sequence alignments are very widely used in all areas of DNA and protein sequence analysis. The main methods that are still in use are based on 'progressive alignment' and date from the mid to late 1980s. Recently, some dramatic improvements have been made to the methodology with respect either to speed and capacity to deal with large numbers ...
Iain M, Wallace +2 more
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