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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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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
core +10 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 +3 more
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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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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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Multiple sequence alignment accuracy and evolutionary distance estimation [PDF]
BMC Bioinformatics, 2005 Background Sequence alignment is a common tool in bioinformatics and comparative genomics. It is generally assumed that multiple sequence alignment yields better results than pair wise sequence alignment, but this assumption has rarely been tested, and ...
Rosenberg Michael S
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Multiple Sequence Alignment Tools on the Web [PDF]
BioTechniques, 2000 The immense number of nucleotide and protein sequences that can be accessed through public databases on the Internet is an invaluable resource to scientists working in the fields of molecular biology, protein chemistry and molecular diagnostics. Tools such as BLAST (1) (also discussed in the March 2000 Internet On-Ramp) and FASTA (7) are used mainly to
Giles J. Gaskell
doaj +4 more sources
MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments [PDF]
BMC Bioinformatics, 2012 Background The generation of multiple sequence alignments (MSAs) is a crucial step for many bioinformatic analyses. Thus improving MSA accuracy and identifying potential errors in MSAs is important for a wide range of post-genomic research.
Collingridge Peter W, Kelly Steven
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A statistical score for assessing the quality of multiple sequence alignments [PDF]
BMC Bioinformatics, 2006 Background Multiple sequence alignment is the foundation of many important applications in bioinformatics that aim at detecting functionally important regions, predicting protein structures, building phylogenetic trees etc.
Aittokallio Tero +3 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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