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
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
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
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
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.
europepmc +2 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 ...
Nicolas Bray, Lior Pachter
arxiv +3 more sources
Kalign 3: multiple sequence alignment of large data sets. [PDF]
Bioinformatics, 2019 Motivation Kalign is an efficient multiple sequence alignment (MSA) program capable of aligning thousands of protein or nucleotide sequences. However, current alignment problems involving large numbers of sequences are exceeding Kalign’s original design ...
Lassmann T.
europepmc +2 more sources
RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency. [PDF]
RNA, 2020 The importance of noncoding RNA sequences has become increasingly clear over the past decade. New RNA families are often detected and analyzed using comparative methods based on multiple sequence alignments.
Wright ES.
europepmc +2 more sources
DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. [PDF]
Bioinformatics, 2020 MOTIVATION The success of genome sequencing techniques has resulted in rapid explosion of protein sequences. Collections of multiple homologous sequences can provide critical information to the modeling of structure and function of unknown proteins ...
Zhang C +4 more
europepmc +2 more sources