Giardia genome resources (GiardiaDB)

Giardia genome resources (GiardiaDB) provides integrated access to genomic-scale datasets and searchable functional genomics queries for the eukaryotic pathogen Giardia lamblia.

Key Features:

• Integrated datasets: Hosts genomic-scale datasets for Giardia lamblia within the EuPathDB framework, consistent with CryptoDB, PlasmoDB, and ToxoDB.
• Searchable database: Maintains fully searchable databases supporting diverse query types.
• BLAST searches: Supports sequence similarity searches using BLAST.
• Annotation and ID searches: Provides annotation keyword searches and gene ID searches.
• Gene Ontology (GO) queries: Enables queries by Gene Ontology terms.
• Sequence motif and protein characteristic searches: Allows searching by sequence motifs and other protein characteristics.
• Expression data queries: Supports functional queries against transcript and protein expression data derived from multiple platforms.
• Phylogenetic analysis: Enables investigation of phylogenetic relationships.
• Query combination: Permits combining results from independent queries to perform complex, genome-wide analyses.
• Query/result storage: Allows storing queries and query results for future reuse.

Scientific Applications:

• Functional genomics: Facilitates comprehensive functional genomic analyses of Giardia lamblia using sequence, annotation, and expression data.
• Gene function and regulation: Enables investigation of gene function and regulation through transcript and protein expression queries.
• Sequence characterization: Supports identification of sequence motifs and assessment of protein characteristics.
• Evolutionary studies: Supports phylogenetic analyses to explore evolutionary relationships.
• Genome-wide integrative analyses: Enables complex, genome-wide studies by combining independent query results.
• Comparative pathogen genomics: Supports cross-species comparisons leveraging integration with other EuPathDB resources (CryptoDB, PlasmoDB, ToxoDB).

Methodology:

Computational methods explicitly include BLAST sequence searches, annotation keyword and gene ID searches, Gene Ontology term queries, sequence motif and protein characteristic searches, querying transcript and protein expression datasets from multiple platforms, phylogenetic relationship analyses, and combining and storing results from independent queries.