PhyloDome

PhyloDome maps phylogenetic distributions of protein domains across eukaryotic taxa to analyze taxonomic spread and lineage-specific variations in multi-domain proteins.

Key Features:

• Phylogenetic distribution overview: Provides a rapid overview of taxonomic spreading and potential interrelations among protein domains, applicable to large datasets with numerous multi-domain proteins.
• Domain input flexibility: Accepts domain names with PFAM and SMART accessions or a set of sequences from which relevant domains are derived.
• Functional and interaction inference: Uses phylogenetic context of domains to aid assignment of protein functions and interactions, supporting comparative analyses such as studies of Hedgehog pathway members in C. elegans.

Scientific Applications:

• Comparative genomics: Characterizes conservation and divergence of protein domains across taxa to infer evolutionary relationships.
• Proteomics: Identifies lineage-specific domain architectures relevant to protein function and complex formation.
• Systems biology: Informs models of pathway composition and potential protein–protein interactions through domain distribution patterns.
• Pathway and interaction analysis: Supports exploration of complex biological pathways and mechanisms by highlighting domain co-occurrence and taxon-specific variations.

Methodology:

Maps phylogenetic distribution of domains from user-defined domain names or sequence sets to analyze taxonomic spread, domain interrelationships, lineage-specific variations, and potential domain interoperability.