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Bioinformatics Advance Access originally published online on April 7, 2005
Bioinformatics 2005 21(12):2906-2908; doi:10.1093/bioinformatics/bti435
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge

Florence Armand 1, Philipp Bucher 2,3, C. Victor Jongeneel 2,4 and Edward E. Farmer 1,*

1Gene Expression Laboratory, Plant Molecular Biology, University of Lausanne Biology Building, 1015 Lausanne, Switzerland
2Swiss Institute of Bioinformatics 1015 Lausanne, Switzerland
3ISREC 1066 Epalinges, Switzerland
4Office of Information Technology, Ludwig Institute for Cancer Research 1015 Lausanne, Switzerland

*To whom correspondence should be addressed.

Summary: Centrifuge is a user-friendly system to simultaneously access Arabidopsis gene annotations and intra- and inter-organism sequence comparison data. The tool allows rapid retrieval of user-selected data for each annotated Arabidopsis gene providing, in any combination, data on the following features: predicted protein properties such as mass, pI, cellular location and transmembrane domains; SWISS-PROT annotations; Interpro domains; Gene Ontology records; verified transcription; BLAST matches to the proteomes of A.thaliana, Oryza sativa (rice), Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. The tool lends itself particularly well to the rapid analysis of contigs or of tens or hundreds of genes identified by high-throughput gene expression experiments. In these cases, a summary table of principal predicted protein features for all genes is given followed by more detailed reports for each individual gene. Centrifuge can also be used for single gene analysis or in a word search mode.

Availability: http://centrifuge.unil.ch/

Contact: edward.farmer{at}unil.ch


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