Saccharomyces genome database (SGD)

Saccharomyces genome database (SGD) provides comprehensive, curated molecular biology and genetics data for Saccharomyces cerevisiae to support genome-scale and gene-level analyses.

Key Features:

• Functional annotations: Curated gene function annotations derived from primary literature.
• Mapping and sequence data: Complete Saccharomyces cerevisiae genomic sequence and associated sequence feature maps.
• Protein domains and structures: PDB Homologs mapping that leverages Protein Data Bank entries to link yeast proteins to structural homologs.
• Motif integration: Motif information integrated from the eMOTIF database.
• Expression profiles: Curated expression data associated with genes and proteins.
• Mutant phenotypes and literature curation: Published phenotypes and supporting literature curated for mutants.
• Physical and genetic interactions: Annotated physical and genetic interaction data for genes and proteins.
• Protein physical and chemical properties: Protein properties and attributes presented for individual gene products.
• Genome-wide comparisons and integrations: Resources to compare and integrate gene- and genome-level features across datasets.
• Fungal Alignment Viewer: Sequence alignments from multiple fungal genomes.
• Sequence Similarity Query: PSI-BLAST-based searches aligning S. cerevisiae proteins to sequences in the NCBI non-redundant protein dataset.
• Yeast Biochemical Pathways: Graphical representation of metabolic pathways grouping genes by metabolic roles.
• Comparative sequence access: Integration of other organism sequences, including Caenorhabditis elegans, for cross-species analyses.
• Protein structure and comparison tools: Integrated tools for structural comparison across eukaryotic proteomes.

Scientific Applications:

• Gene function annotation: Interpreting gene functions and linking genes to phenotypes using curated annotations and mutant data.
• Structural biology and homology inference: Mapping yeast proteins to PDB homologs to infer structure–function relationships.
• Comparative genomics and evolutionary studies: Cross-species sequence comparisons and alignments across fungal genomes and other organisms such as C. elegans.
• Metabolic and pathway analysis: Assigning genes to pathways and analyzing metabolic roles using the Yeast Biochemical Pathways resource.
• Interaction network analysis: Studying genetic and physical interaction networks to elucidate functional relationships.
• Sequence similarity and evolutionary inference: Using PSI-BLAST searches against the NCBI non-redundant dataset to identify homologs and infer evolutionary relationships.

Methodology:

Sequence similarity searches using PSI-BLAST against the NCBI non-redundant protein dataset; sequence alignments from multiple fungal genomes via the Fungal Alignment Viewer; PDB homology mapping using Protein Data Bank entries; motif integration from eMOTIF; graphical grouping of genes into metabolic pathways.