HMMER hmmscan (EBI)

HMMER hmmscan (EBI) performs protein sequence similarity searches using profile hidden Markov models (profile HMMs) to identify homologs and annotate protein families against databases such as Pfam.

Key Features:

• Probabilistic profile HMM searches: Uses profile hidden Markov models to detect sequence homology and assign protein family membership.
• HMMER3 algorithmic improvements: Implements HMMER3 algorithms that provide up to 100-fold speed improvements over previous versions for profile HMM searches.
• Versatile search modes: Supports single-sequence searches, searches of multiple-sequence alignments or profiles against databases, and searches specifically against the Pfam HMM database.
• Batch query support: Accepts multiple queries for high-throughput sequence analysis.
• Programmatic integration: Provides RESTful and SOAP APIs for integration into scripted and automated workflows.
• EMBL-EBI Job Dispatcher integration: Operates within the EMBL-EBI Job Dispatcher framework and interoperates with resources such as UniProt, InterPro, ENA, and Ensembl Genomes.

Scientific Applications:

• Homology detection: Identify homologous proteins across species using profile HMM matches.
• Protein family annotation: Annotate protein functions and domains by matching sequences to Pfam profiles.
• Large-scale genomic and proteomic analyses: Enable high-throughput analysis of sequence datasets for comparative genomics and proteomics.

Methodology:

Performs probabilistic sequence comparisons using HMMER3 implementations of profile hidden Markov models to search query sequences or alignments against databases of profile HMMs (e.g., Pfam).