Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge.

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Serval ID
serval:BIB_B5B5A7754746
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge.
Journal
Bioinformatics
Author(s)
Armand F., Bucher P., Jongeneel C.V., Farmer E.E.
ISSN
1367-4803 (Print)
ISSN-L
1367-4803
Publication state
Published
Issued date
2005
Peer-reviewed
Oui
Volume
21
Number
12
Pages
2906-2908
Language
english
Abstract
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@unil.ch.
Keywords
Arabidopsis/genetics, Arabidopsis/metabolism, Arabidopsis Proteins/genetics, Arabidopsis Proteins/metabolism, Chromosome Mapping/methods, Computer Graphics, Gene Expression Profiling/methods, Software, User-Computer Interface
Pubmed
Web of science
Open Access
Yes
Create date
24/01/2008 15:39
Last modification date
25/09/2019 6:10
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