hmmsim (genouest)

hmmsim (genouest) performs profile hidden Markov model (profile HMM) searches on protein sequences using the HMMER3 engine to detect sequence similarity and support protein annotation and comparative analyses.

Key Features:

• HMMER3 engine and performance: Implements the HMMER3 software suite providing up to a 100-fold increase in search speed for profile HMM computations.
• Profile HMM searches: Executes profile HMM–sequence and sequence–profile comparisons for sensitive detection of homologous regions.
• Search modes: Supports searching a single protein sequence against a target sequence database and scanning multiple sequence alignments or profile HMMs against a target sequence database.
• Pfam integration: Enables comparison of protein sequences against the Pfam database for domain and family annotation.
• Programmatic access: Exposes search methods via RESTful web services for integration into scripted workflows.

Scientific Applications:

• Homology detection: Identifies homologous proteins across species through sensitive profile HMM comparisons.
• Protein annotation: Assigns domain and family annotations to unknown protein sequences by comparison with Pfam profiles and profile HMMs.
• Evolutionary and functional inference: Supports investigation of evolutionary relationships and functional predictions based on sequence similarity and domain architecture.

Methodology:

Uses HMMER3 to perform profile HMM-based sequence and profile comparisons, including queries against Pfam, and exposes these methods via RESTful web services.