Results 1 to 10 of about 429,505 (261)

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
doaj   +2 more sources

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, Szabó Adrienn, Miklós István, Hein Jotun   +3 more
doaj   +2 more sources

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, Umi Kalsom Yusof, Taiseer Abdalla Elfadil Eisa, Maged Nasser   +3 more
doaj   +2 more sources

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, Xiaolei Zhang, Manuel Gil, Maria Anisimova   +3 more
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Three-Way Alignment Improves Multiple Sequence Alignment of Highly Diverged Sequences [PDF]

Algorithms
The standard approach for constructing a phylogenetic tree from a set of sequences consists of two key stages. First, a multiple sequence alignment (MSA) of the sequences is computed.
Mahbubeh Askari Rad, Alibek Kruglikov, Xuhua Xia   +2 more
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A layout framework for genome-wide multiple sequence alignment graphs [PDF]

Frontiers in Bioinformatics
Sequence 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, Jeremias Schebera, Dirk Zeckzer, Daniel Wiegreffe   +3 more
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Scalable long read self-correction and assembly polishing with multiple sequence alignment. [PDF]

Sci Rep, 2021
Morisse P, Marchet C, Limasset A, Lecroq T, Lefebvre A.   +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, Baqiao Liu, Kelly P. Williams, Tandy Warnow   +3 more
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Efficient Multiple Sequences Alignment Algorithm Generation via Components Assembly Under PAR Framework

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, Haipeng Shi, Haihe Shi, Shenghua Xu   +3 more
doaj   +1 more source

Strategies for Multiple Sequence Alignment

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, Alexander J. Ropelewski, David W. Deerfield   +2 more
doaj   +1 more source