MAFFT-DASH: Integrated protein sequence and structural alignment

570Citations
Citations of this article
399Readers
Mendeley users who have this article in their library.

This article is free to access.

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.

References Powered by Scopus

MAFFT multiple sequence alignment software version 7: Improvements in performance and usability

31106Citations
N/AReaders
Get full text

BLAST+: Architecture and applications

13369Citations
N/AReaders
Get full text

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

11295Citations
N/AReaders
Get full text

Cited by Powered by Scopus

Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins

1245Citations
N/AReaders
Get full text

SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses

393Citations
N/AReaders
Get full text

Recent developments of HDAC inhibitors: Emerging indications and novel molecules

258Citations
N/AReaders
Get full text

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Cite

CITATION STYLE

APA

Rozewicki, J., Li, S., Amada, K. M., Standley, D. M., & Katoh, K. (2019). MAFFT-DASH: Integrated protein sequence and structural alignment. Nucleic Acids Research, 47(W1), W5–W10. https://doi.org/10.1093/nar/gkz342

Readers' Seniority

Tooltip

PhD / Post grad / Masters / Doc 120

72%

Researcher 26

16%

Lecturer / Post doc 12

7%

Professor / Associate Prof. 8

5%

Readers' Discipline

Tooltip

Biochemistry, Genetics and Molecular Bi... 92

54%

Agricultural and Biological Sciences 59

35%

Immunology and Microbiology 11

6%

Computer Science 8

5%

Save time finding and organizing research with Mendeley

Sign up for free