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Bioinformatics Advance Access published online on March 15, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti380
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received January 28, 2005
Accepted March 6, 2005

Applications note

Mips bacterial genomes functional annotation benchmark dataset

Igor V. Tetko 1*, Barbara Brauner 1, Irmtraud Dunger-Kaltenbach 1, Goar Frishman 1, Corinna Montrone 1, Gisela Fobo 1, Andreas Ruepp 1, Alexey V. Antonov 1, Dimitrij Surmeli 1, and Hans W. Mewes 1

1 Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health, Ingolstaedter Landstr. 1, D-85764 Neuherberg, Germany

* To whom correspondence should be addressed.
Igor V. Tetko, E-mail: i.tetko{at}gsf.de


  Abstract

Motivation: Any development of new methods for automatic functional annotation of proteins according to their sequences requires high-quality data (as benchmark) as well as tedious preparatory work to generate sequence parameters required as input data for the machine learning methods. Different program settings and incompatible protocols make a comparison of the analyzed methods difficult.

Results: The MIPS Bacterial Functional Annotation Benchmark data set (MIPS-BFAB) is a new high-quality resource comprising four bacterial genomes manually annotated according to the MIPS Functional Catalogue (FunCat). These resources include pre-calculated sequence parameters such as sequence similarity scores, InterPro domain composition and other parameters that could be used to develop and bench-mark methods for functional annotation of bacterial protein sequences. These data are provided in XML format and can be used by scientists who are not necessarily experts in genome annotation.

Availability: BFAB is available at http://mips.gsf.de/proj/bfab.


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