AmoebaDB

AmoebaDB provides functional genomic data and query capabilities for Amoebozoa by hosting genome sequences and expression data for Entamoeba species (E. dispar, E. invadens, E. histolytica) to support comparative, functional, pathogenesis, and evolutionary studies.

Key Features:

• Genomic Content: Genome sequences are provided for Entamoeba species E. dispar, E. invadens, and E. histolytica.
• Expression Data: Microarray expression data specifically for E. histolytica are included.
• Graphical Strategy Builder: A graphical strategy builder enables construction and execution of complex, multi-step queries that integrate multiple data types.
• Query Capabilities: Genomic-scale queries support BLAST searches, annotation keywords, gene IDs, Gene Ontology (GO) terms, sequence motif searches, protein characteristic filters, phylogenetic relationship queries, and transcript and protein expression profile queries.
• EuPathDB Integration: AmoebaDB is maintained within the EuPathDB Bioinformatics Resource Center framework.

Scientific Applications:

• Comparative Genomics: Enables identification of conserved and species-specific genomic elements across Entamoeba genomes.
• Functional Genomics: Supports integration of expression data with genome annotations to infer gene function and regulation.
• Pathogenesis Studies: Facilitates investigation of genes involved in virulence, host interaction, and immune evasion in E. histolytica.
• Evolutionary Biology: Allows cross-species comparisons to study evolutionary trajectories and adaptations among Entamoeba species.

Methodology:

Supports BLAST searches, Gene Ontology-term queries, sequence motif searches, filters by protein characteristics and phylogenetic relationships, and integration of microarray transcript and protein expression data via a graphical strategy builder.