HSDatabase

HSDatabase provides a curated repository of highly similar duplicate genes (HSDs) across eukaryotic nuclear genomes to support studies of gene duplication and its role in adaptation in model animals, land plants, and algae.

Key Features:

• Extensive Collection: Houses 117,864 curated HSDs from 40 distinct genomes with statistics on HSD counts per genome and details on individual HSD copy numbers and lengths.
• Sequence Alignments: Provides sequence alignments for duplicate gene copies to enable comparison of genetic similarities and differences.
• Downloadable Sequences: Supplies downloadable sequences of gene copies for downstream analyses.
• Integration with Genome Browsers: Links HSD entries to genome browsers to provide genomic context and visualization.
• Linkage to Other Databases: Connects HSD records to Pfam and the Kyoto Encyclopedia of Genes and Genomes (KEGG) for functional annotation and pathway analysis.
• Homology Search Tool: Includes a Basic Local Alignment Search Tool (BLAST) option for identifying potential homologous sequences within and across species.

Scientific Applications:

• Comparative Genomics: Supports comparative analyses of gene duplicates across species to assess conservation and divergence of HSDs.
• Evolutionary Biology: Facilitates studies of gene duplication as an evolutionary mechanism contributing to genetic novelty and adaptation.
• Gene Dosage and Adaptation: Enables investigation of how HSDs contribute to organismal adaptation to extreme conditions via gene dosage effects.
• Integration with HSDFinder: Enhances identification, annotation, categorization, and visualization of HSDs through integration with HSDFinder.

Methodology:

Collection and curation of HSDs from nuclear genomes across multiple species using bioinformatics techniques to identify and categorize highly similar duplicate genes.