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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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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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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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HELIOS: High-speed sequence alignment in optics.
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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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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An enhanced RNA alignment benchmark for sequence alignment programs
Algorithms for Molecular Biology, 2006 Background The performance of alignment programs is traditionally tested on sets of protein sequences, of which a reference alignment is known. Conclusions drawn from such protein benchmarks do not necessarily hold for the RNA alignment problem, as was ...
Steger Gerhard +2 more
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Continuous Action Recognition Based on Sequence Alignment [PDF]
, 2014 Continuous action recognition is more challenging than isolated recognition because classification and segmentation must be simultaneously carried out.
Cech, Jan +3 more
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