WDAC

WDAC assigns weighted domain architectures to proteins to improve detection of homologs by comparing the sequential order of domains and weighting domains by abundance and versatility for more accurate homology inference.

Key Features:

• Domain Weighting: Assigns weight scores to domains based on abundance and versatility extracted from RefSeq proteins to distinguish promiscuous/mobile domains from conventional domains.
• Similarity Measurement: Measures similarity between domain architectures using information-retrieval algorithms including cosine similarity, the Goodman-Kruskal gamma function, and a domain duplication index, and integrates these into a composite similarity score.
• Integration with Sequence Similarity: Combines domain architecture comparison with sequence similarity assessments to strengthen identification of proteins sharing the same domain architecture and to detect distant homologies among multidomain proteins.

Scientific Applications:

• Homology Identification: Identifies homologs of multidomain proteins using weighted domain architectures and outperforms unweighted domain architecture comparison (DAC) methods for such cases.
• Functional Annotation Transfer: Facilitates transfer of functional annotations from characterized homologous proteins to newly discovered proteins, particularly those with complex or multiple domains.

Methodology:

Compute domain weights from RefSeq proteins based on domain abundance and versatility to flag promiscuous/mobile domains; compute domain-architecture similarities using cosine similarity, Goodman-Kruskal gamma, and domain duplication index; integrate these measures into a composite similarity score and combine the domain-architecture similarity with sequence similarity.