Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees
By Kazunori D. Yamada, Kentaro Tomii, Kazutaka Katoh. Bioinform., 2016
320 citations recorded by the source corpus.
Motivation: Large multiple sequence alignments (MSAs), consisting of thousands of sequences, are becoming more and more common, due to advances in sequencing technologies. The MAFFT MSA program has several options for building large MSAs, but their performances have not been sufficiently assessed yet, because realistic benchmarking of large MSAs has been difficult. Recently, such assessments have been made possible through the HomFam and ContTest benchmark protein datasets. Along with the development of these datasets, an interesting theory was proposed: chained guide trees increase the accuracy of MSAs of structurally conserved regions. This theory challenges the basis of progressive alignment methods and needs to be examined by being compared with other known methods including computationally intensive ones. Results: We used HomFam, ContTest and OXFam (an extended version of OXBench) to evaluate several methods enabled in MAFFT: (1) a progressive method with approximate guide trees, (2) a progressive method with chained guide trees, (3) a combination of an iterative refinement method and a progressive method and (4) a less approximate progressive method that uses a rigorous guide tree and consistency score. Other programs, Clustal Omega and UPP, available for large MSAs, were also included into the comparison. The effect of method 2 (chained guide trees) was positive in ContTest but negative in HomFam and OXFam. Methods 3 and 4 increased the benchmark scores more consistently than method 2 for the three datasets, suggesting that they are safer to use. Availability and Implementation: http://mafft.cbrc.jp/alignment/software/ Contact: katoh@ifrec.osaka-u.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/58c25cf2148b79b8a337d186513e1c0194465a6f
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In Molecular Biology
- Daron M. Standley
- Kazutaka Katoh
- John Rozewicki
- Karlou Mar Amada
- Songling Li
- B. Faircloth
- Robert C. Edgar
- Steven Kelly
Citations in the corpus
- Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice (2019, unknown): “Subsequently, fragments were inserted to 16S rRNA gene context by q2-fragment-insertion (Janssen et al., 2018) and alignments were obtained using MAFFT (Yamada et al., 2016) and a phylogenetic tree was generated using FastTree (Price et al., 2009).”
- MAFFT-DASH: integrated protein sequence and structural alignment (2019, background): “HomFam and OXFam were chosen over raw HOMSTRAD and OXBench because they contain more information about reliably aligned regions (27) that can be used for more accurate scoring of estimated alignments.”