A simple method to control over-alignment in the MAFFT multiple sequence alignment program

Abstract

Motivation: We present a new feature of the MAFFT multiple alignment program for suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly sensitive in aligning conserved regions in remote homologs, but the risk of over-alignment is recently becoming greater, as low-quality or noisy sequences are increasing in protein sequence databases, due, for example, to sequencing errors and difficulty in gene prediction.Results: The proposed method utilizes a variable scoring matrix for different pairs of sequences (or groups) in a single multiple sequence alignment, based on the global similarity of each pair. This method significantly increases the correctly gapped sites in real examples and in simulations under various conditions. Regarding sensitivity, the effect of the proposed method is slightly negative in real protein-based benchmarks, and mostly neutral in simulation-based benchmarks. This approach is based on natural biological reasoning and should be compatible with many methods based on dynamic programming for multiple sequence alignment.Availability and implementation: The new feature is available in MAFFT versions 7.263 and higher. http://mafft.cbrc.jp/alignment/software/Contact: katoh@ifrec.osaka-u.ac.jpSupplementary information: Supplementary data are available at Bioinformatics online.

Identification of endophytic fungi from leaves of Pandanaceae based on their morphotypes and DNA sequence data from southern Thailand

“…Raw forward and reverse sequences were assembled using Geneious Pro.v4.8.5. Sequence alignments were carried out with MAFFT v.6.864b (Katoh and Standley 2016) and alignments were manually improved where necessary. The sequence datasets were combined using BioEdit v.7.2.5 (Hall 2004 …”

Three new Hermatomyces species (Lophiotremataceae) on Pandanus odorifer from Southern Thailand

“…Raw forward and reverse sequences were assembled using Geneious. Pro.v4.8.5 and sequence alignments were done with MAFFT v.6.864b (Katoh & Standley 2016) and alignments were manually improved if necessary. The sequence datasets were combined using BioEdit v.7.2.5 (Hall 2004).…”

Muyocopron garethjonesii sp. nov. (Muyocopronales, Dothideomycetes) on Pandanus sp.

“…Lichenothelia convexa Henssen 1987 (L1607) was used as the outgroup taxon (Table 1). All sequence alignments were done with MAFFT v.6.864b (Katoh & Standley 2016) and alignments were manually improved if necessary. The sequence datasets were combined using BioEdit v.7.2.5 (Hall 2004).…”