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Open Access Highly Accessed Database

e-Fungi: a data resource for comparative analysis of fungal genomes

Cornelia Hedeler1*, Han Min Wong3, Michael J Cornell1, Intikhab Alam1, Darren M Soanes3, Magnus Rattray1, Simon J Hubbard2, Nicholas J Talbot3, Stephen G Oliver4 and Norman W Paton1

Author Affiliations

1 School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK

2 Faculty of Life Sciences, The University of Manchester, Manchester, M13 9PT, UK

3 School of Biosciences, University of Exeter, Exeter, EX4 4QD, UK

4 Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK

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BMC Genomics 2007, 8:426  doi:10.1186/1471-2164-8-426

Published: 20 November 2007

Abstract

Background

The number of sequenced fungal genomes is ever increasing, with about 200 genomes already fully sequenced or in progress. Only a small percentage of those genomes have been comprehensively studied, for example using techniques from functional genomics. Comparative analysis has proven to be a useful strategy for enhancing our understanding of evolutionary biology and of the less well understood genomes. However, the data required for these analyses tends to be distributed in various heterogeneous data sources, making systematic comparative studies a cumbersome task. Furthermore, comparative analyses benefit from close integration of derived data sets that cluster genes or organisms in a way that eases the expression of requests that clarify points of similarity or difference between species.

Description

To support systematic comparative analyses of fungal genomes we have developed the e-Fungi database, which integrates a variety of data for more than 30 fungal genomes. Publicly available genome data, functional annotations, and pathway information has been integrated into a single data repository and complemented with results of comparative analyses, such as MCL and OrthoMCL cluster analysis, and predictions of signaling proteins and the sub-cellular localisation of proteins. To access the data, a library of analysis tasks is available through a web interface. The analysis tasks are motivated by recent comparative genomics studies, and aim to support the study of evolutionary biology as well as community efforts for improving the annotation of genomes. Web services for each query are also available, enabling the tasks to be incorporated into workflows.

Conclusion

The e-Fungi database provides fungal biologists with a resource for comparative studies of a large range of fungal genomes. Its analysis library supports the comparative study of genome data, functional annotation, and results of large scale analyses over all the genomes stored in the database. The database is accessible at http://www.e-fungi.org.uk webcite, as is the WSDL for the web services.