Volume 14 Supplement 17

Proceedings of the 12th Annual UT-ORNL-KBRIN Bioinformatics Summit 2013

Open Access

FPD2GB2: Automating a transition from a customized genome browser to GBrowse2

  • Roger Chui1,
  • Jerzy W Jaromczyk1,
  • Neil Moore1 and
  • Christopher L Schardl2
BMC Bioinformatics201314(Suppl 17):A17

https://doi.org/10.1186/1471-2105-14-S17-A17

Published: 22 October 2013

Background

We present FPD2GB2, a collection of scripts to automate data migration of a custom genome database and browser to a new implementation. The fungal endophytes genome project (http://www.endophyte.uky.edu/) hosted at the University of Kentucky uses a custom genome browser and database to support several genome sequencing, annotation, and analysis projects. This system is currently based around a locally-developed genome annotation database, visualized using the GBrowse version 1 genome browser together with a large amount of custom code that supports metadata and rendering features not supported by GBrowse 1. Since our initial development of our genome site, a newer version of GBrowse, version 2, has been released. Unlike GBrowse version 1, version 2 supports a very expressive database schema based on the standardized GFF3 format. This schema natively supports the types of data that we currently store in our custom database. In order to simplify maintenance, to ease the upgrade path to future versions of GBrowse, and to improve interoperability with software and websites that support GBrowse and the GFF3 format, we have decided to migrate our custom database to the GFF3 format supported by GBrowse 2. This migration allows us to simplify and in some cases even eliminate much of our custom code. We discuss the challenges presented by such a data migration task, and describe the FPD2GB2 script collection we developed to automate the process.

Declarations

Acknowledgements

This work was partially supported by NIGMS Grant 1R01GM086888-01, Kentucky NSF-EPSCoR Grant 0814194, NSF Grant EF-0523661, and USDA-NRA Grant 2005-35319-16141.

Authors’ Affiliations

(1)
Department of Computer Science, University of Kentucky
(2)
Department of Plant Pathology, University of Kentucky

Copyright

© Chui et al; licensee BioMed Central Ltd. 2013

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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