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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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Developments in Algorithms for Sequence Alignment: A Review [PDF]
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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Sequence‐to‐sequence alignment using a pendulum [PDF]
IET Computer Vision, 2015 Analysing two or more video sequences of dynamic scenes typically requires time synchronisation between sequences, where this alignment is not always possible using hardware.
Tomislav Pribanic +2 more
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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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Optimal sequence alignments [PDF]
Proceedings of the National Academy of Sciences, 1983 Current theory is adequate to the task of finding an optimal alignment between two character strings such as nucleic acids. Most algorithms currently in use must fail to find the homologous alignment between a set of codons for the chicken α- and β-hemoglobin sequence when it is in fact discoverable by a more general treatment of gaps.
Walter M. Fitch, Temple F. Smith
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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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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 ...
Kun-Mao Chao +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 ...
Desmond G. Higgins +2 more
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