Skip Navigation


Bioinformatics Advance Access originally published online on April 7, 2005
Bioinformatics 2005 21(12):2906-2908; doi:10.1093/bioinformatics/bti435
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/12/2906    most recent
bti435v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Armand, F.
Right arrow Articles by Farmer, E. E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Armand, F.
Right arrow Articles by Farmer, E. E.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.