d-Omix

d-Omix integrates analysis of protein domain architectures to compare domain combinations, construct domain-architecture-based phylogenetic trees, compute domain graphs, and infer protein interaction networks using DOMINE for studies of protein function, interaction, and evolution.

Key Features:

• InterProScan input support: Accepts InterProScan files as primary input and can generate InterProScan outputs from raw protein sequences.
• Phylogenetic tree construction from DAs: Constructs phylogenetic trees from distance matrices derived from protein domain architectures (DAs) and enables comparison with sequence-based phylogenetic trees.
• Domain graph calculation: Calculates domain versatility, abundance, and co-presence and represents these relationships in a domain graph.
• DA alignment similarity: Compares proteins using alignments of domain architectures to assess structural similarity beyond sequence comparisons.
• Protein network construction: Infers putative protein networks using domain–domain interactions sourced from DOMINE (Database of Molecular Interactions).
• Domain search tool support: Supports domain search tools such as hmmpfam and superfamily for domain annotation.

Scientific Applications:

• Protein function analysis: Enables analysis of domain combinations to infer functional roles and structural determinants of proteins.
• Interaction network inference: Supports generation of hypotheses for protein–protein interactions and pathway associations via domain–domain interactions.
• Evolutionary and phylogenetic studies: Facilitates comparison of domain-architecture-based and sequence-based phylogenies to study the evolution of domain combinations and adaptations.
• Proteomics comparative analysis: Allows comparative analysis of protein datasets to investigate domain distribution and co-occurrence patterns.

Methodology:

Computational methods include parsing InterProScan outputs (or generating them from sequences), calculating distance matrices from protein domain architectures (DAs) for phylogenetic tree construction, performing domain-architecture alignments for similarity comparisons, computing domain versatility/abundance/co-presence and generating domain graphs, and inferring protein networks from DOMINE domain–domain interactions; supports domain searches via hmmpfam and superfamily.