MMseqs2 desktop and local web server app for fast, interactive sequence searches

Milot Mirdita; Martin Steinegger; Johannes Söding

doi:10.1093/bioinformatics/bty1057

MMseqs2 desktop and local web server app for fast, interactive sequence searches

Bioinformatics. 2019 Aug 15;35(16):2856-2858. doi: 10.1093/bioinformatics/bty1057.

Authors

Milot Mirdita¹, Martin Steinegger^{1

2}, Johannes Söding¹

Affiliations

¹ Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
² Department of Chemistry, Seoul National University, Seoul, Korea.

Abstract

Summary: The MMseqs2 desktop and web server app facilitates interactive sequence searches through custom protein sequence and profile databases on personal workstations. By eliminating MMseqs2's runtime overhead, we reduced response times to a few seconds at sensitivities close to BLAST.

Availability and implementation: The app is easy to install for non-experts. GPLv3-licensed code, pre-built desktop app packages for Windows, MacOS and Linux, Docker images for the web server application and a demo web server are available at https://search.mmseqs.com.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Sequence
Computers*
Databases, Factual
Software*