MMseqs2 desktop and local web server app for fast, interactive sequence searches
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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.
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From ColabFold - Making protein folding accessible to all (2021) · cites this paper as [11]
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From Fast and accurate protein structure search with Foldseek (2024) · cites this paper as [43]
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Self-citation
- Authors
- Mirdita, M., Steinegger, M., & Söding, J.
- Affiliations
- Max Planck Institute for Biophysical Chemistry (DE)
- Seoul National University (KR)
- Corresponding author
- Steinegger, Martin
- Söding, Johannes
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-01-07
- Volume
- 35
- Issue
- 16
- Pages
- 2856-2858
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC6691333
- OpenAlex
- W2951149542
- Cited by
- 618
- References
- 11
- Citations by year
- 2026: 98 · 2025: 112 · 2024: 156 · 2023: 109 · 2022: 104 · 2021: 23 · 2020: 14 · 2019: 2
- FWCI
- 11.83
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion, cc-by)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Seoul National University Open Repository (Seoul National University) (submittedVersion)
- Funders
- European Research Council
- Horizon 2020 Framework Programme (Virus-X, 685778)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- MMseqs2, protein sequence search, desktop application, web server, BLAST comparison, search response time, Docker
- MeSH terms
- Amino Acid Sequence, Computers, Software, Databases, Factual
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