MAFFT-DASH: integrated protein sequence and structural alignment

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ID: 305902
2019
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Abstract
Here, we describe a web server that integrates structural alignments with the MAFFT multiple sequence alignment (MSA) tool. For this purpose, we have prepared a web-based Database of Aligned Structural Homologs (DASH), which provides structural alignments at the domain and chain levels for all proteins in the Protein Data Bank (PDB), and can be queried interactively or by a simple REST-like API. MAFFT-DASH integration can be invoked with a single flag on either the web (https://mafft.cbrc.jp/alignment/server/) or command-line versions of MAFFT. In our benchmarks using 878 cases from the BAliBase, HomFam, OXFam, Mattbench and SISYPHUS datasets, MAFFT-DASH showed 10–20% improvement over standard MAFFT for MSA problems with weak similarity, in terms of Sum-of-Pairs (SP), a measure of how well a program succeeds at aligning input sequences in comparison to a reference alignment. When MAFFT alignments were supplemented with homologous sequences, further improvement was observed. Potential applications of DASH beyond MSA enrichment include functional annotation through detection of remote homology and assembly of template libraries for homology modeling.
Reference Key
openalex_W2944021648 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors John Rozewicki, Songling Li, Karlou Mar Amada, Daron M. Standley, Kazutaka Katoh
Journal Nucleic Acids Research
Year 2019
DOI
10.1093/nar/gkz342
URL
https://academic.oup.com/nar/article-pdf/47/W1/W5/28880182/gkz342.pdf
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