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Progressive multiple sequence alignment with indel evolution [PDF]
BMC Bioinformatics, 2018 Background Sequence alignment is crucial in genomics studies. However, optimal multiple sequence alignment (MSA) is NP-hard. Thus, modern MSA methods employ progressive heuristics, breaking the problem into a series of pairwise alignments guided by a ...
Massimo Maiolo +3 more
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Recursive MAGUS: Scalable and accurate multiple sequence alignment. [PDF]
PLoS Computational Biology, 2021 Multiple sequence alignment tools struggle to keep pace with rapidly growing sequence data, as few methods can handle large datasets while maintaining alignment accuracy.
Vladimir Smirnov
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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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Scaling statistical multiple sequence alignment to large datasets [PDF]
BMC Genomics, 2016 Background Multiple sequence alignment is an important task in bioinformatics, and alignments of large datasets containing hundreds or thousands of sequences are increasingly of interest.
Michael Nute, Tandy Warnow
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A layout framework for genome-wide multiple sequence alignment graphs [PDF]
Frontiers in BioinformaticsSequence alignments are often used to analyze genomic data. However, such alignments are often only calculated and compared on small sequence intervals for analysis purposes.
Jeremias Schebera +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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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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Algorithms for normalized multiple sequence alignments [PDF]
, 2021 Sequence alignment supports numerous tasks in bioinformatics, natural language processing, pattern recognition, social sciences, and others fields. While the alignment of two sequences may be performed swiftly in many applications, the simultaneous alignment of multiple sequences proved to be naturally more intricate.
arxiv +1 more source
Accelerated large-scale multiple sequence alignment
BMC Bioinformatics, 2011 Background Multiple sequence alignment (MSA) is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Prior MSA acceleration attempts with reconfigurable computing have only addressed the first stage of ...
Lloyd Scott, Snell Quinn O
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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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