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HMMER web server: 2026 update
Aleksandar Rajković1, Martin Beracochea1, Alexander B Rogers1
1EMBL-EBI European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.
Nucleic Acids Research
|April 27, 2026
Summary
The HMMER web server has been updated with a reengineered interface and infrastructure to improve protein analysis performance and reliability. It now offers enhanced user experience and better support for large-scale sequence similarity searches and annotations.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- The HMMER web server provides access to the HMMER software suite for protein analysis using profile hidden Markov models.
- Exponential growth in sequence databases necessitates infrastructure improvements for performance and reliability.
Purpose of the Study:
- To reengineer the HMMER web server for enhanced user experience and improved performance.
- To support programmatic access and efficient handling of large-scale database searches.
Main Methods:
- Complete reengineering of the web interface using modern web technologies (JavaScript, React).
- Rewriting the web application programming interface (API) with updated endpoints and JSON responses.
- Redesigning the infrastructure for horizontal scaling and asynchronous job processing.
Main Results:
- Enhanced user experience with session-based search history and streamlined results visualization.
- Improved programmatic access via a rewritten API.
- Efficient handling of searches against significantly larger databases.
Conclusions:
- The updated HMMER web server offers a more robust and user-friendly platform for protein sequence analysis.
- The improvements ensure continued service reliability and performance speed despite growing data volumes.
- The server remains free and open to all users without login requirements.
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