Comprehensive yeast genome database (CYGD)

Comprehensive yeast genome database (CYGD) provides integrated sequence, functional annotation, and interaction data for Saccharomyces cerevisiae to support analysis of molecular structure and functional networks in yeast.

Key Features:

• Interaction coverage: Comprehensive cataloging of physical and functional interactions among proteins and other genetic elements in S. cerevisiae.
• Cellular networks: Representation of metabolic pathways, regulatory mechanisms, signal transduction processes, transport systems, and clusters of co-regulated genes.
• Gene and protein annotation: Detailed sequence data and functional annotations for individual genes and proteins beyond basic annotation.
• Comparative genomics: Facilitation of comparative genomic analysis with related yeast species and use of S. cerevisiae as a reference model to streamline annotation of newly sequenced genomes.
• SIMAP integration: Inclusion of SIMAP (Similarity Matrix of Proteins) to aid exploration and comparison of related genomes using the S. cerevisiae backbone.

Scientific Applications:

• Gene function prediction: Use of curated annotations and interaction data to infer functions of genes and proteins.
• Pathway analysis: Analysis of metabolic and regulatory pathways and their components within yeast cells.
• Genetic interaction studies: Investigation of genetic interactions and co-regulation within cellular networks.
• Comparative and evolutionary genomics: Examination of evolutionary relationships and functional similarities across different yeast species.
• Systems biology: Support for systems-level analyses of molecular structure and functional networks in eukaryotic cells using yeast as a model.

Methodology:

Uses SIMAP (Similarity Matrix of Proteins) to explore and compare related genomes using the S. cerevisiae genome as a backbone and employs S. cerevisiae–based reference annotation to streamline annotation of newly sequenced genomes.