Genome Database for Rosaceae (GDR)

Genome Database for Rosaceae (GDR) provides a centralized relational database of genetic and genomic data for the Rosaceae family to support genomics and genetics research.

Key Features:

• Comprehensive Data Collection: Contains publicly available Rosaceae sequences and annotated EST databases from peach, strawberry, almond and other rosaceous species including apple, pear, cherry, peach, almond, and rose, and includes a genetically anchored peach physical map.
• Integrated Mapping Tools: Integrates mapping resources including CMap (comparative map viewer) and WebFPC/WebChrom for the peach physical map.
• Advanced Query Capabilities: Supports queries of ESTs, BACs, markers, and traits by multiple categories with results cross-referenced to mapping resources.
• Sequence Analysis Tools: Provides a sequence similarity server supporting BLAST and FASTA, a batch BLAST/FASTA server for GDR datasets, a sequence assembly server, and microsatellite and primer detection tools.
• Annotation Features: Assembles ESTs into unigene sets for each genus and the Rosaceae family with annotations including contig assembly, putative function, simple sequence repeats, open reading frames, single nucleotide polymorphisms, gene ontology terms, and anchored map positions.

Scientific Applications:

• Gene discovery: Facilitates gene discovery and genetic characterization across Rosaceae species using curated sequence and annotation data.
• Comparative and physical mapping: Enables anchoring of sequences to physical and genetic maps and comparative mapping across species using sequence similarity searches and integrated mapping resources.

Methodology:

Uses sequence similarity searches with BLAST and FASTA; EST assembly into unigene sets and sequence assembly; identification of simple sequence repeats and primer sites; contig assembly, ORF detection, SNP identification, assignment of gene ontology terms, and integration with CMap and WebFPC/WebChrom and a genetically anchored peach physical map.