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Updated: Jun 18, 2026
09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
The Pfam protein families database
Robert D Finn1, Jaina Mistry, John Tate
1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK. rdf@sanger.ac.uk
Nucleic Acids Research
|November 19, 2009
Summary
The Pfam database now uses HMMER3 for protein family and domain analysis, offering 100x speed improvements and enhanced sensitivity. This update, Pfam release 24.0, includes 11,912 families with significant recent revisions.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Pfam is a comprehensive database for protein families and domains.
- Previous versions relied on HMMER2 for profile hidden Markov model analysis.
Purpose of the Study:
- To detail major updates in Pfam release 24.0.
- To highlight the transition to HMMER3 and its implications.
Main Methods:
- Implementation of HMMER3, a significantly faster and more sensitive profile hidden Markov model package.
- Routine use of the forward algorithm for improved detection sensitivity.
Main Results:
- Pfam release 24.0 incorporates HMMER3, resulting in approximately 100-fold speed enhancement.
- Increased sensitivity in protein domain and family identification.
- The database now contains 11,912 protein families, with many updated in the last two years.
Conclusions:
- The adoption of HMMER3 represents a substantial advancement for the Pfam database.
- These updates enhance the efficiency and accuracy of protein family and domain analysis.
- Pfam remains a critical resource, accessible globally through multiple servers.
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01:24Protein Organization
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