hmmsearch (genouest)

hmmsearch (genouest) performs profile hidden Markov model (profile HMM) searches using HMMER3 to detect and score homologous protein sequences in sequence databases such as Pfam for protein sequence analysis and annotation.

Key Features:

• HMMER3 backend: Uses the HMMER3 software suite to implement probabilistic profile HMM methods for sequence comparison.
• Speed and efficiency: Reports substantially increased processing speed relative to predecessors, enabling rapid database searches.
• Versatile search capabilities: Supports single protein sequence analysis, multiple protein sequence alignments, profile HMMs searched against target sequence databases, and protein sequence searches against Pfam databases.
• RESTful web services: Exposes search methods as RESTful web services for integration into scripted workflows.
• Result formats: Produces tabular outputs and graphical summaries to report matches and search statistics.

Scientific Applications:

• Homology detection: Identifies homologous proteins across different species through profile HMM scoring.
• Protein characterization: Characterizes novel proteins by comparing sequences against known profile HMMs and Pfam profiles.
• Evolutionary analysis: Investigates evolutionary relationships via multiple sequence alignments and profile comparisons.
• Functional annotation: Supports functional annotation of genes within genomic datasets by assigning matches to profile HMMs and Pfam families.

Methodology:

Implements probabilistic profile hidden Markov model searches using the HMMER3 suite to query profile HMMs against sequence databases including Pfam and exposes methods via RESTful web services, returning tabular and graphical summaries.