hmmalign (genouest)

hmmalign (genouest) aligns protein sequences to profile hidden Markov models (profile HMMs) to generate multiple-sequence alignments that support protein similarity detection and functional annotation.

Key Features:

• Profile HMM alignment: Aligns query sequences to profile hidden Markov models for sensitive multiple-sequence alignment.
• HMMER integration: Implements algorithms from the HMMER suite, including HMMER3 performance optimizations.
• Probabilistic sequence similarity: Uses probabilistic methods to assess protein sequence similarity against profile HMMs.
• Versatile search modes: Supports aligning single or multiple protein sequence alignments, searching profile HMMs against target sequence databases, and querying individual protein sequences against the Pfam database.
• Batch processing: Accepts and processes multiple queries in a single operation for large-scale analyses.
• Programmatic access: Exposes functionality via RESTful web services for integration into scripted workflows.

Scientific Applications:

• Homology detection: Identifies homologous proteins through profile HMM-based alignment and similarity scoring.
• Evolutionary analysis: Supports inference of evolutionary relationships via multiple-sequence alignments derived from profile HMMs.
• Functional annotation: Aids annotation of protein function by mapping sequences to Pfam families and profile HMM models.
• Protein database searches: Enables systematic similarity searches across protein sequence databases using profile HMMs.

Methodology:

Performs sequence-to-profile alignments using profile hidden Markov models and probabilistic scoring implemented in the HMMER suite (HMMER3 optimizations noted).