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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
doaj +5 more sources
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.
Gambin, Anna, Otto, Rafał
core +9 more sources
MAVID: Constrained ancestral alignment of multiple sequences [PDF]
arXiv, 2003 We describe a new global multiple alignment program capable of aligning a large number of genomic regions. Our progressive alignment approach incorporates the following ideas: maximum-likelihood inference of ancestral sequences, automatic guide-tree construction, protein based anchoring of ab-initio gene predictions, and constraints derived from a ...
Bray, Nicolas, Pachter, Lior
arxiv +9 more sources
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
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
europepmc +2 more sources
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.
Araujo, Eloi +3 more
arxiv +5 more sources
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
europepmc +2 more sources
Multiple sequence alignment based on set covers [PDF]
Lecture Notes in Computer Science 3907 (2006), 127-137, 2004 We introduce a new heuristic for the multiple alignment of a set of sequences. The heuristic is based on a set cover of the residue alphabet of the sequences, and also on the determination of a significant set of blocks comprising subsequences of the sequences to be aligned.
A. Bahr +15 more
arxiv +4 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
doaj +2 more sources
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