Kinetoplastid genome resources (TritryPDB)

Kinetoplastid genome resources (TritryPDB) provide integrated access to genome-scale datasets and annotations for kinetoplastid parasites to support comparative genomics, functional genomics, and genome annotation improvement.

Key Features:

• Integrated genome-scale datasets: Aggregates genome annotations and functional genomics datasets for kinetoplastid parasites, including many community-contributed and pre-publication datasets.
• Computational infrastructure: Built on the GUS/WDK computational infrastructure developed by the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org).
• GeneDB integration: Incorporates genome annotation and analyses from GeneDB alongside other functional genomics data.
• Species coverage: Includes datasets for Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei, and T. cruzi.
• Genomic context browsing: Enables inspection of individual genes and chromosomal spans within their genomic context.
• Synteny alignments: Provides syntenic alignments between kinetoplastid organisms to support evolutionary and comparative analyses.
• Search strategy system: Supports construction of complex queries that combine multiple data types and stores search strategies for future access.
• Searchable user annotations: Captures 'User Comments' on gene pages that become searchable via text search and are forwarded to curators for potential incorporation into reference annotations.

Scientific Applications:

• Comparative genomics and synteny: Analysis of syntenic alignments to infer evolutionary relationships among kinetoplastid species.
• Functional genomics integration: Cross-referencing functional genomics datasets with genome annotations to analyze gene function and expression.
• Genome annotation curation: Improvement and curation of reference annotations using GeneDB data, community-contributed datasets, and searchable user comments.
• Cross-study and longitudinal queries: Integrated searches across studies or time points using stored complex search strategies.

Methodology:

Data integration and query infrastructure are implemented using the GUS/WDK system from EuPathDB.org, incorporating GeneDB annotations and functional genomics datasets, with stored search strategies and text-searchable user comments forwarded to curators.