webPRC

webPRC performs profile–profile comparisons of profile hidden Markov models (HMMs) to detect distant homologous relationships and annotate protein domains.

Key Features:

• Profile–profile comparison: Performs profile–profile comparisons of HMMs derived from multiple sequence alignments.
• PRC scoring and alignment: Implements Profile Comparer (PRC) scoring and alignment of HMMs.
• Database searches: Searches HMMs against domain databases such as CATH and Pfam-domain.
• Output formats: Produces aligned HMMs and multiple sequence alignments as results.
• Jalview integration: Integrates with Jalview for inspection and editing of output alignments.
• Logo generation: Generates sequence logos from aligned HMMs and from multiple sequence alignments.

Scientific Applications:

• Distant homologue detection: Detection of remote evolutionary relationships between protein families via profile–profile comparisons.
• Protein domain annotation: Annotation and characterization of protein domains using aligned HMMs and sequence logos.
• Comparative evolutionary analysis: Evaluation and comparison of multiple sequence alignments and HMM alignments to infer evolutionary relationships.
• Database-wide homology searches: Searching for and identifying homologues across CATH and Pfam-domain HMM databases.

Methodology:

Computationally, webPRC performs profile–profile comparisons by scoring and aligning HMMs derived from multiple sequence alignments using Profile Comparer (PRC) (PMID: 19420063); it searches against CATH and Pfam HMM databases, outputs aligned HMMs and multiple sequence alignments, generates sequence logos, and integrates with Jalview for alignment inspection and editing.