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This site collects ressources that can be used to benchmark and to develop new annotation methods. The manual annotation data of four bacterial genomes, Bacillus subtilis, Helicobacter pylori, Listeria innocua and Listeria monocytogenes as well as some sequence parameters are available in XML format for download. The annotation was performed using FunCat (Ruepp et al, 2004). We suggest that all users estimate the performance of their methods using the leave-one-genome-out schema.

We encourage authors to deposit their XML files with results, algorithms and scripts used to evaluate methods on this site. Sample annotations according to the highest sequence similarity scores of BLAST, PSI-BLAST and FASTA methods are provided. If you use some data from this site, please refer to the methods that were used to generate the sequence parameters (indicated in the XML file with data) and to the server itself (Tetko et al, 2005).

Tetko, I.V.; Brauner, B.; Dunger-Kaltenbach, I.; Frishman, G.; Montrone, C.; Fobo, G.; Ruepp, A.; Antonov, A.V.; Surmeli, D. & Mewes, H.W. (2005) MIPS Bacterial Genomes Functional Annotation Benchmark Dataset, Bioinformatics, 21, 2520-2521.

Ruepp, A.; Zollner, A.; Maier, D.; Albermann, K.; Hani, J.; Mokrejs, M.; Tetko, I.; Guldener, U.; Mannhaupt, G.; Munsterkotter, M. & Mewes, H. W. (2004). The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res, 32, 5539-45.

Surmeli, D.; Ratmann, O.; Mewes, H.W.; Tetko; I.V. (2008) FunCat functional inference with belief propagation and feature integration. Comput Biol Chem. 2008 32(5):375-377, preprint download.

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