hmmconvert (genouest)

hmmconvert (genouest) converts profile Hidden Markov Model (HMM) file formats to enable compatibility among bioinformatics tools and to support model-based protein family analysis, multiple sequence alignment, and database searches.

Key Features:

• Profile HMM Conversion: Converts between various profile HMM file formats to ensure compatibility across bioinformatics tools and databases.
• Application in Protein Analysis: Estimates HMM parameters from unaligned sequences to generate multiple sequence alignments and model protein families such as the globin family, protein kinase catalytic domains, and EF-hand calcium-binding motifs.
• Database Searching Capability: Uses constructed HMMs to search sequence databases such as SWISS-PROT for family members or domain occurrences.
• Accuracy in Discrimination Tests: Distinguishes members and non-members of protein families with high accuracy in discrimination tests, outperforming PROSITE in classification tasks.
• Advantage Over PROFILESEARCH: Trains HMMs from unaligned sequences to reduce false negatives and false positives compared with PROFILESEARCH, which requires aligned training data.

Scientific Applications:

• Multiple Sequence Alignment: Generates alignments that closely match those derived from three-dimensional structural information.
• Protein Family Identification: Identifies and annotates protein family members to support classification and evolutionary analysis.
• Functional Domain Discovery: Detects functional domains such as EF-hand calcium-binding motifs, exemplified by identification within L-type calcium channels.

Methodology:

Estimates HMM parameters from sets of unaligned sequences and uses the resulting HMMs for multiple sequence alignment and database searches.