The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes - PubMed (original) (raw)

. 2004 Oct 14;32(18):5539-45.

doi: 10.1093/nar/gkh894. Print 2004.

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The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes

Andreas Ruepp et al. Nucleic Acids Res. 2004.

Abstract

In this paper, we present the Functional Catalogue (FunCat), a hierarchically structured, organism-independent, flexible and scalable controlled classification system enabling the functional description of proteins from any organism. FunCat has been applied for the manual annotation of prokaryotes, fungi, plants and animals. We describe how FunCat is implemented as a highly efficient and robust tool for the manual and automatic annotation of genomic sequences. Owing to its hierarchical architecture, FunCat has also proved to be useful for many subsequent downstream bioinformatic applications. This is illustrated by the analysis of large-scale experiments from various investigations in transcriptomics and proteomics, where FunCat was used to project experimental data into functional units, as 'gold standard' for functional classification methods, and also served to compare the significance of different experimental methods. Over the last decade, the FunCat has been established as a robust and stable annotation scheme that offers both, meaningful and manageable functional classification as well as ease of perception.

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References

    1. Endy D. and Brent,R. (2001) Modelling cellular behaviour. Nature, 409, 391–395. - PubMed
    1. Barrett A.J. (1997) Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB). Enzyme Nomenclature. Recommendations 1992. Supplement 4: corrections and additions. Eur. J. Biochem., 250, 1–6. - PubMed
    1. Saier M.H. (2000) A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol. Mol. Biol. Rev., 64, 354–411. - PMC - PubMed
    1. Bairoch A. and Apweiler,R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45–48. - PMC - PubMed
    1. Barker W.C., Garavelli,J.S., Huang,H.Z., McGarvey,P.B., Orcutt,B.C., Srinivasarao,G.Y., Xiao,C.L., Yeh,L.S.L., Ledley,R.S., Janda,J.F. et al. (2000) The protein information resource (PIR). Nucleic Acids Res., 28, 41–44. - PMC - PubMed

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