PartiGeneDB

PartiGeneDB organizes species-specific non-redundant partial eukaryotic gene sets assembled from 1.83 million survey sequences across 247 eukaryotic organisms to enable comparative genomics, gene expression analysis, and identification of conserved genetic elements.

Key Features:

• Non-Redundant Gene Objects: Collates and processes survey sequence data into species-specific, non-redundant gene objects termed "partial genomes".
• Assembled Dataset: Contains assembled partial genomes derived from 1.83 million sequences across 247 eukaryotic organisms.
• Query Capabilities: Supports sequence similarity searches and text queries based on BLAST annotations.
• Data Visualization: Provides the Java-based SimiTri tool to represent sequence similarity relationships among large numbers of sequences in a single graphic.
• Regular Incremental Updates: Accommodates periodic addition of new sequence datasets for newly studied and existing species.

Scientific Applications:

• Comparative Genomics: Enables comparison of gene content and similarity across diverse eukaryotic lineages using partial genomes.
• Gene Expression Studies: Supports analysis of gene expression patterns inferred from survey sequence datasets.
• Conserved Element Identification: Facilitates detection of conserved genetic elements across taxa.
• Evolutionary Biology: Supports evolutionary analyses by organizing partial-genome data for lineage-wide comparisons.

Methodology:

Collation and assembly of survey sequence data into species-specific, non-redundant gene objects ("partial genomes"); use of BLAST annotations for sequence similarity searches and text queries; visualization of sequence similarity relationships via the Java-based SimiTri tool; and support for regular incremental updates with new sequence datasets.