HAMAP

HAMAP annotates protein sequences by classifying them into manually curated family profiles and applying expert-crafted functional annotation rules to produce high-quality, standardized annotations comparable to UniProtKB/Swiss-Prot.

Key Features:

• Manually curated family profiles: Curated sequence-family profiles are used to classify proteins and capture family-specific information, with 1983 family classification profiles as of 2014-09-03 (previously 1780).
• Annotation rules: Expert-crafted functional annotation rules employ complex logic to enable precise annotations of individual variants, with 1998 rules as of 2014-09-03 (previously 1720).
• Taxonomic coverage: Profiles and rules cover bacterial, archaeal, and eukaryotic organisms.
• Integration with UniRule/UniProtKB/TrEMBL: Integrated into the UniRule pipeline of UniProt to provide automated annotations for millions of unreviewed UniProtKB/TrEMBL sequences.
• Sequence-profile search algorithm: Uses an advanced sequence-profile search algorithm to match protein sequences to family profiles.
• Published resource: Growth and enhancements reported in the literature (PMID: 25348399), noting substantial expansion since 2013.

Scientific Applications:

• Automated annotation of UniProtKB/TrEMBL: Provides detailed functional annotations for millions of unreviewed protein sequences in UniProtKB/TrEMBL.
• Protein family classification: Assigns sequences to specific sequence families across bacteria, archaea, and eukaryotes.
• Variant-specific functional annotation: Distinguishes and annotates functional differences among individual variants within large homologous protein families.
• Support for large-scale annotation pipelines: Contributes standardized annotations to UniProt automated annotation workflows via the UniRule pipeline.

Methodology:

HAMAP applies manually curated family sequence profiles and an advanced sequence-profile search algorithm to classify proteins, then applies expert-crafted annotation rules with complex logic and integrates results into the UniRule pipeline.