hmmstat (genouest)

hmmstat (genouest) analyzes protein sequences using profile hidden Markov models (profile HMMs) to perform profile HMM searches and generate statistical summaries for domain and family identification.

Key Features:

• Speed and Efficiency: Implements HMMER3, providing an approximately 100-fold speed improvement for rapid execution of profile HMM searches against large protein sequence databases.
• Versatile Search Capabilities: Supports single protein sequence searches, multiple protein sequence alignment searches, profile HMM searches against target sequence databases, and protein sequence searches against the Pfam database.
• RESTful Web Services Integration: Exposes search functionalities as RESTful web services to enable integration into scripted workflows.
• Comprehensive Result Presentation: Produces tabular results and graphical summaries to facilitate appraisal of search outcomes.

Scientific Applications:

• Protein sequence similarity searches: Identification of homologous proteins using profile HMM-based searches.
• Functional annotation of proteins: Assignment of putative functions based on domain and family matches detected by profile HMMs.
• Identification of protein domains and families: Detection and characterization of protein domains and families, including searches against Pfam.
• Comparative genomics studies: Comparison of protein domain and family content across genomes using profile HMM profiles.

Methodology:

Performs profile hidden Markov model searches using the HMMER software suite (HMMER3) and returns tabular and graphical summaries with search functions exposed via RESTful web services.