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

By Kazutaka Katoh, John Rozewicki, Kazunori D. Yamada. 2017

7,650 citations recorded by the source corpus.

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.

Subfields: Artificial Intelligence, Molecular Biology

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Citations in the corpus

Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival (2018, methodology): “The representative sequences were aligned using the MAFFT webservice (G-INS-i option and an un-align level of 0.4; Katoh et al., 2017).”
Bifidobacteria-mediated immune system imprinting early in life (2020, methodology): “Phylogenic alignments were conducted with mafft (Katoh, 2019) and fasttree (Price, 2009) and Shannon Diversity and a Weighted Unifrac distance matrix (Lozupone, 2010) were created using the q2-diversity plugin in qiime2, rarified to theminimumnumber of dereplicated sequences passing quality filter f”
Analysis of insertions and extensions in the functional evolution of the ribonucleotide reductase family (2022, methodology): “To analyze the C-terminal extensions, the sequences from the class II clade in the tree were aligned with MAFFT.55 Due to the absence of the sequence of the only structurally characterized dimeric class II RNR from T. maritima in the tree, a pair-wise alignment between the sequence of T. maritima cl”
Monkeypox Virus in Nigeria: Infection Biology, Epidemiology, and Evolution (2020, methodology): “The genomes were aligned with MAFFT version 7 [174].”
A structural inventory of native ribosomal ABCE1‐43S pre‐initiation complexes (2020, neutral): “The models of tRNA i (PDB 6FEC, Eliseev et al , 2018), eIF2 α , and eIF2 γ (PDB 6O85, Kenner et al , 2019) and the homology models of eIF2 β and eIF1 (based on PDB 6GSM) were fitted into the map and adjusted using Coot.”
Fungal diversity notes 709–839: taxonomic and phylogenetic contributions to fungal taxa with an emphasis on fungi on Rosaceae (2018, methodology): “The sequences were aligned in MAFFT v. 7 at the web server (http://mafft.cbrc.jp/align ment/server) (Kuraku et al. 2013; Katoh et al. 2017).”
Auto-antibodies against type I IFNs in patients with life-threatening COVID-19 (2020, methodology): “471 software ( 33 ), using the L-INS-i strategy ( 34 ) and the BLOSUM62 scoring matrix for amino acid substitutions.”