HAMAP-Scan

HAMAP-Scan annotates and classifies protein sequences by scanning them against manually curated HAMAP family profiles and applying expert-curated annotation rules to generate UniProtKB-format annotations.

Key Features:

• Profile-Based Classification: Uses a library of manually curated HAMAP family profiles for protein sequence family classification, comprising 1,983 profiles (as of September 2014).
• Expert-Curated Annotation Rules: Applies 1,998 expert-crafted annotation rules to assign detailed functional annotations and discriminate functional variants within homologous families.
• Integration with UniProt Systems: Operates within the UniRule pipeline of UniProt to support large-scale annotation of unreviewed sequences in UniProtKB/TrEMBL.
• Improved Sequence-Profile Search Algorithm: Incorporates an improved sequence-profile search algorithm to enhance the efficiency and accuracy of sequence classification and annotation.

Scientific Applications:

• Protein Function Prediction: Provides function predictions for proteins in datasets by mapping sequences to HAMAP profiles and applying annotation rules.
• Genomic Annotation Projects: Enables annotation of whole genomes or all open reading frames (ORFs) using HAMAP profiles and rules.
• Functional Variant Analysis: Identifies and annotates functional variants within large homologous protein families.
• Large-Scale Database Annotation: Facilitates annotation of millions of unreviewed sequences in UniProtKB/TrEMBL through integration with UniRule.

Methodology:

HAMAP-Scan scans input protein sequences or entire genomes against the HAMAP family profile library and annotates sequence matches using the associated expert-curated rules to produce UniProtKB-format annotations.