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.


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

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*