hmmfetch (genouest)

hmmfetch (genouest) retrieves profile Hidden Markov Models (HMMs) from HMM files and enables profile HMM-based protein sequence similarity searches using the HMMER3 probabilistic framework.

Key Features:

• Speed and efficiency: Implements HMMER3 improvements yielding up to a 100-fold speed gain compared to previous versions.
• Supported query types: Accepts single protein sequences, multiple sequence alignments, or profile HMMs as queries against target sequence databases.
• Pfam integration: Supports searches of protein sequences against the Pfam database to identify protein families and domains.
• Batch processing and RESTful services: Supports batch submission of multiple queries and exposes search methods as RESTful web services for programmatic access.

Scientific Applications:

• Homology detection: Identification of homologous proteins through profile HMM similarity searches.
• Protein function annotation: Annotation of protein function via matches to profile HMMs and Pfam entries.
• Evolutionary analysis: Exploration of evolutionary relationships among proteins using profile HMM comparisons.

Methodology:

Retrieves profile HMMs from HMM files and applies the probabilistic profile HMM algorithms implemented in HMMER3 to perform sequence similarity searches.