HMMER phmmer (EBI)

HMMER phmmer (EBI) performs protein sequence similarity searches using profile hidden Markov models (profile HMMs) to detect homologous sequences and support protein annotation and evolutionary analysis.

Key Features:

• Profile HMM-based searches: Implements profile hidden Markov models (profile HMMs) for sensitive protein sequence similarity detection.
• HMMER3 performance: Uses the HMMER3 implementation, providing an approximately 100-fold speed gain over previous iterations.
• Versatile query types: Supports searching one or more sequences, multiple protein sequence alignments, or profile HMMs against target sequence databases and comparing single protein sequences to the Pfam database.
• Batch processing: Supports submission and processing of multiple queries in a single execution.
• Programmatic APIs: Exposes search methods via RESTful and SOAP web service APIs for remote execution and integration into scripted workflows.
• Integration with EMBL-EBI resources: Integrated into the EMBL-EBI Job Dispatcher framework and can target sequence resources such as UniProt, InterPro, ENA, and Ensembl Genomes.

Scientific Applications:

• Homology detection: Identify homologous protein sequences across sequence databases.
• Protein annotation: Support protein annotation by detecting matches to Pfam and similar sequence entries.
• Evolutionary analysis: Explore evolutionary relationships among proteins through detected homologs.
• Genomics, proteomics, and systems biology: Apply sequence similarity results in genomics, proteomics, and systems biology studies.

Methodology:

Performs profile HMM-based protein sequence similarity searches using the HMMER3 implementation, accepting sequences, multiple sequence alignments, or profile HMMs as queries and searching target sequence databases (including Pfam and resources such as UniProt, InterPro, ENA, and Ensembl Genomes); search methods are provided via RESTful and SOAP web service APIs.