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This article is part of the supplement: UT-ORNL-KBRIN Bioinformatics Summit 2009

Open Access Meeting abstract

Visualizing and sharing results in bioinformatics projects: GBrowse and GenBank exports

Elissaveta G Arnaoudova1, Philip J Bowens1, Roger G Chui1, Randy D Dinkins2, Uljana Hesse3, Jerzy W Jaromczyk1*, Mitchell Martin1, Paul Maynard1, Neil Moore1 and Chris L Schardl3

Author affiliations

1 Department of Computer Science, University of Kentucky, Lexington, KY 40506, USA

2 United States Department of Agriculture, Agriculture Research Service, University of Kentucky Campus, Lexington, KY 40546, USA

3 Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA

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Citation and License

BMC Bioinformatics 2009, 10(Suppl 7):A4  doi:10.1186/1471-2105-10-S7-A4


The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2105/10/S7/A4


Published:25 June 2009

© 2009 Arnaoudova et al; licensee BioMed Central Ltd.

Background

Effective tools for presenting and sharing data are necessary for collaborative projects, typical for bioinformatics. In order to facilitate sharing our data with other genomics, molecular biology, and bioinformatics researchers, we have developed software to export our data to GenBank and combined the export utilities with our customized and augmented version of GBrowse. The GBrowse bioinformatics software provides a way for users to graphically view genomic feature data stored in a back-end database. GenBank is an open-access database, maintained by the National Center for Biotechnology Information (NCBI), containing annotated versions of all publicly available DNA sequences. To support exports relevant to our data, we have developed a tool that processes a list of expressed sequence tags (ESTs), correlates these tags with information from our database, and constructs a set of files for batch submission to the GenBank EST database (dbEST).

We are using this tool in combination with our Epichloe festucae genome database (Figure 1), used also as a back-end for GBrowse, to prepare dbEST submissions for the transcriptome of the fungal endophyte E. festucae, as well as one of its host plants, Festuca pratensis (meadow fescue). ESTs from infected plants are compared against the fungal genome sequence using alignment tools such as Exonerate. We are using this tool to prepare batch EST submissions of 35,000 fungal and 75,000 plant ESTs, containing a total of 32 million and 60 million base pairs, respectively. The software can be adapted for use with other bioinformatics projects.

thumbnailFigure 1. GBrowse for the Epichloe festucae genome project.

Acknowledgements

We acknowledge funding from the KBRIN-INBRE NIH P20RR16481, the NIGMS R01GM086888, USDA-NRI 2005-35319-16141, NSF EF-0523661, and Kentucky NSF-EPSCoR.