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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Reticular alignment: A progressive corner-cutting method for multiple sequence alignment [PDF]
BMC Bioinformatics, 2010 Background In this paper, we introduce a progressive corner cutting method called Reticular Alignment for multiple sequence alignment. Unlike previous corner-cutting methods, our approach does not define a compact part of the dynamic programming table ...
Novák Ádám +3 more
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Enhanced Genetic Method for Optimizing Multiple Sequence Alignment [PDF]
Mathematics, 2023 In the realm of bioinformatics, Multiple Sequence Alignment (MSA) is a pivotal technique used to optimize the alignment of multiple biological sequences, guided by specific scoring criteria.
Mohammed K. Ibrahim +3 more
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Advances in post-processing methods for multiple sequence alignment [PDF]
Frontiers in GeneticsThe reliability of multiple sequence alignment (MSA) results directly determines the credibility of the conclusions drawn from biological research. However, MSA is inherently an NP-hard problem, making it theoretically impossible to guarantee a globally ...
Yixiao Zhai +3 more
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An enhanced algorithm for multiple sequence alignment of protein sequences using genetic algorithm [PDF]
, 2015 One of the most fundamental operations in biological sequence analysis is multiple sequence alignment (MSA). The basic of multiple sequence alignment problems is to determine the most biologically plausible alignments of protein or DNA sequences. In this
Kumar, Manish
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An Improved Search Algorithm for Optimal Multiple-Sequence Alignment
, 2011 Multiple sequence alignment (MSA) is a ubiquitous problem in computational biology. Although it is NP-hard to find an optimal solution for an arbitrary number of sequences, due to the importance of this problem researchers are trying to push the limits ...
Schroedl, S.
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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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Scalable long read self-correction and assembly polishing with multiple sequence alignment. [PDF]
Sci Rep, 2021 Morisse P +4 more
europepmc +3 more sources
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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