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Bioinformatics Advance Access published online on April 7, 2005
Bioinformatics, 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@oupjournals.org
Received December 3, 2004
Revised March 22, 2005
Accepted April 5, 2005

Applications note

Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge

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

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

* To whom correspondence should be addressed.
Edward E. Farmer, E-mail: edward.farmer{at}unil.ch


  Abstract

Summary: Centrifuge is a user-friendly system with which 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, O. sativa (rice), C. elegans, D. melanogaster and H. 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 prinicpal 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/.


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