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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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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MAGUS: Multiple sequence Alignment using Graph clUStering. [PDF]
Bioinformatics, 2021 Motivation The estimation of large multiple sequence alignments (MSAs) is a basic bioinformatics challenge. Divide-and-conquer is a useful approach that has been shown to improve the scalability and accuracy of MSA estimation in established methods such ...
Smirnov V, Warnow T.
europepmc +2 more sources
OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy [PDF]
BMC Bioinformatics, 2003 Background The alignment of two or more protein sequences provides a powerful guide in the prediction of the protein structure and in identifying key functional residues, however, the utility of any prediction is completely dependent on the accuracy of ...
Searle Stephen MJ +4 more
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Scalable long read self-correction and assembly polishing with multiple sequence alignment. [PDF]
Sci Rep, 2021 Third-generation sequencing technologies allow to sequence long reads of tens of kbp, that are expected to solve various problems. However, they display high error rates, currently capped around 10%.
Morisse P +4 more
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MUSCLE: a multiple sequence alignment method with reduced time and space complexity [PDF]
BMC Bioinformatics, 2004 BackgroundIn a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reported to date on four alignment accuracy
R. C. Edgar
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ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference. [PDF]
PLoS Biol, 2020 Highly divergent sites in multiple sequence alignments (MSAs), which can stem from erroneous inference of homology and saturation of substitutions, are thought to negatively impact phylogenetic inference.
Steenwyk JL +4 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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MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. [PDF]
Brief Bioinform, 2019 This article describes several features in the MAFFT online service for multiple sequence alignment (MSA). As a result of recent advances in sequencing technologies, huge numbers of biological sequences are available and the need for MSAs with large ...
Katoh K, Rozewicki J, Yamada KD.
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Contextual Multiple Sequence Alignment [PDF]
BioMed Research International, 2005 In a recently proposed contextual alignment model, efficient algorithms exist for global and local pairwise alignment of protein sequences. Preliminary results obtained for biological data are very promising. Our main motivation was to adopt the idea of context dependency to the multiple‐alignment setting.
Anna Gambin, Rafał Otto
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