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      MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

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          Abstract

          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 numbers of sequences is increasing. To extract biologically relevant information from such data, sophistication of algorithms is necessary but not sufficient. Intuitive and interactive tools for experimental biologists to semiautomatically handle large data are becoming important. We are working on development of MAFFT toward these two directions. Here, we explain (i) the Web interface for recently developed options for large data and (ii) interactive usage to refine sequence data sets and MSAs.

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          Most cited references 29

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          Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era.

          Recently developed methods have shown considerable promise in predicting residue-residue contacts in protein 3D structures using evolutionary covariance information. However, these methods require large numbers of evolutionarily related sequences to robustly assess the extent of residue covariation, and the larger the protein family, the more likely that contact information is unnecessary because a reasonable model can be built based on the structure of a homolog. Here we describe a method that integrates sequence coevolution and structural context information using a pseudolikelihood approach, allowing more accurate contact predictions from fewer homologous sequences. We rigorously assess the utility of predicted contacts for protein structure prediction using large and representative sequence and structure databases from recent structure prediction experiments. We find that contact predictions are likely to be accurate when the number of aligned sequences (with sequence redundancy reduced to 90%) is greater than five times the length of the protein, and that accurate predictions are likely to be useful for structure modeling if the aligned sequences are more similar to the protein of interest than to the closest homolog of known structure. These conditions are currently met by 422 of the protein families collected in the Pfam database.
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            A beginner's guide to eukaryotic genome annotation.

            The falling cost of genome sequencing is having a marked impact on the research community with respect to which genomes are sequenced and how and where they are annotated. Genome annotation projects have generally become small-scale affairs that are often carried out by an individual laboratory. Although annotating a eukaryotic genome assembly is now within the reach of non-experts, it remains a challenging task. Here we provide an overview of the genome annotation process and the available tools and describe some best-practice approaches.
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              CLUSTAL: a package for performing multiple sequence alignment on a microcomputer.

              An approach for performing multiple alignments of large numbers of amino acid or nucleotide sequences is described. The method is based on first deriving a phylogenetic tree from a matrix of all pairwise sequence similarity scores, obtained using a fast pairwise alignment algorithm. Then the multiple alignment is achieved from a series of pairwise alignments of clusters of sequences, following the order of branching in the tree. The method is sufficiently fast and economical with memory to be easily implemented on a microcomputer, and yet the results obtained are comparable to those from packages requiring mainframe computer facilities.
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                Author and article information

                Journal
                Brief Bioinform
                Brief. Bioinformatics
                bib
                Briefings in Bioinformatics
                Oxford University Press
                1467-5463
                1477-4054
                July 2019
                06 September 2017
                06 September 2017
                : 20
                : 4
                : 1160-1166
                Author notes
                Corresponding author: Kazutaka Katoh, 3-1 Yamadaoka, Suita, Osaka 565-0871, JAPAN. E-mail: katoh@ 123456ifrec.osaka-u.ac.jp
                Article
                bbx108
                10.1093/bib/bbx108
                6781576
                28968734
                © The Author 2017. Published by Oxford University Press.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

                Page count
                Pages: 7
                Product
                Funding
                Funded by: Japan Society for the Promotion of Science 10.13039/501100001691
                Award ID: JP16K07464
                Funded by: Japan Agency for Medical Research and Development 10.13039/100009619
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