Clustal Omega (EBI)

Clustal Omega (EBI) performs multiple sequence alignments of amino acid or nucleotide sequences to infer positional homology for evolutionary, functional, and structural analyses.

Key Features:

• Guide trees and HMM profile-profile techniques: Constructs guide trees and applies Hidden Markov Model (HMM) profile–profile techniques for alignment.
• External HMMs and iterative refinement: Supports incorporation of external HMMs and iterative refinement to enhance alignment accuracy.
• Full alignment generation: Produces full multiple sequence alignments from unaligned input sequences.
• Scalability: Scales to handle large and high-throughput sequence datasets efficiently.
• EMBL-EBI integration: Integrates with the EMBL-EBI Job Dispatcher framework and interoperates with databases such as UniProt, InterPro, ENA, and Ensembl Genomes.

Scientific Applications:

• Evolutionary relationships: Aligning homologous sequences to study evolutionary relationships.
• Functional genomics: Aligning sequences to support functional genomics investigations.
• Protein structure prediction: Providing residue-level alignments used in protein structure prediction.
• High-throughput sequence analysis: Enabling analysis of large-scale sequencing datasets and high-throughput workflows.

Methodology:

Clustal Omega constructs guide trees and uses HMM profile–profile techniques to produce full alignments from unaligned sequences and supports external HMMs and iterative refinement to improve accuracy.