AspGD comparative genomics pipelines and visualization tools

Jennifer Russo Wortman1, Jonathan Crabtree1, Marcus C. Chibucos1, Joshua Orvis1, Martha B. Arnaud2, Maria C. Costanzo2, Diane O. Inglis2, Prachi Shah2, Marek S. Skrzypek2, and Gavin Sherlock2

Author address: 

1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 2Department of Genetics, Stanford University, Stanford, CA

Abstract: 

The Aspergillus Genome Database (http://www.aspgd.org/) is an online genomic resource for Aspergillus genomics and molecular biology, with information curated from the literature and web-based research tools for exploration and analysis of these data. With ten annotated genome sequences from eight Aspergillus species publicly available, and more on the way, our goals include leveraging comparative genomics for annotation improvement, and providing sophisticated querying and visualization tools to maximize the utility of these data. The Aspergillus genomes were annotated at different institutions using diverse methods over an extended time frame, during which available tools and datasets have evolved. Common annotation inconsistencies include missed gene calls, gene truncations, failure to predict small exons, and inappropriate gene merges. We are developing a standard, optimized pipeline across all Aspergillus genomes, comprehensively incorporating new data as it becomes available and leveraging comparative genomics analyses to improve protein-coding gene prediction. Resulting annotations will be integrated into AspGD, along with ortholog and synteny data linking knowledge across the Aspergilli. Otholog and synteny data are currently available at the AspGD website through data downloads as well as interactively through the Sybil software infrastructure. Sybil is an open source, web-based software package for visualizing and mining comparative genomics data (http://sybil.sf.net). Powered by a Chado relational database (http://www.gmod.org/schema), Sybil provides an extensive set of interfaces for interrogating multi-genome comparisons at varying levels of resolution from the whole genome scale to individual loci. Sybil allows users to search for genes, clusters or genomic regions and visualize the results in a comparative genomic context, along with syntenic relationships and annotated features of interest. Configurable reports are available through the web interface, supporting the identification of core and accessory genes from all or a subset of available genomes. Reports and displays are interactive and linked, allowing seamless navigation from a chromosome view, to a cluster report, to an individual protein page. All of the data in AspGD are freely available to the public from http://www.aspgd.org/. AspGD is supported by grant RO1 AI077599 from the NIAID at the NIH.
2010

abstract No: 

NULL

Full conference title: 

10th EUROPEAN CONFERENCE ON FUNGAL GENETICS
    • ECFG 10th (2010)