GOssTo

GOssTo computes semantic similarities between gene products using Gene Ontology annotations to assess functional relatedness.

Key Features:

• Semantic Similarity Measures: Implements six distinct semantic similarity measures encompassing both term-based and graph-based approaches for assessing functional relatedness.
• Random Walk Contribution: Computes the Random Walk Contribution for any chosen measure to refine and improve the accuracy of similarity assessments.
• High-Throughput Capability: Optimized for speed to enable semantic similarity calculations on genomic-scale datasets.
• Extensibility: Supports extension by adding new similarity measures to accommodate evolving research needs.

Scientific Applications:

• Functional Genomics: Infers functional relationships between genes and assists in annotation of uncharacterized proteins using GO-based similarity.
• Comparative Genomics: Facilitates comparative analyses across species by identifying conserved gene functions through GO similarity scores.
• Network Analysis: Supports construction and analysis of biological networks based on functional similarity between gene products.

Methodology:

Uses six term-based and graph-based semantic similarity measures and computes a Random Walk Contribution to refine similarity scores.