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

Cornelia Hedeler*, Han Min Wong, Michael J. Cornell, Intikhab Alam, Darren M. Soanes, Magnus Rattray, Simon J. Hubbard, Nicholas J. Talbot, Stephen G. Oliver, Norman W. Paton

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

35 Scopus citations

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, as is the WSDL for the web services.

Original languageEnglish (US)
Article number426
JournalBMC genomics
Volume8
DOIs
StatePublished - Nov 20 2007
Externally publishedYes

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Fingerprint

Dive into the research topics of 'e-Fungi: A data resource for comparative analysis of fungal genomes'. Together they form a unique fingerprint.

Cite this