By Julio Collado-Vides, Ralf Hofestädt

Are the eyes homologous? -- Automation of protein series characterization and its program in complete proteome research -- info fusion and metabolic community keep an eye on -- Specificity of protein-DNA interactions -- Genomics of gene rules: the view from Escherichia coli -- Discovery of DNA regulatory motifs -- Gene networks description and modeling within the GeneNet method -- law of mobile states in mammalian cells from a genomewide view -- Predicting protein functionality and networks on a genomewide scale -- Metabolic pathways -- towards machine simulation of the entire telephone

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Sonnhammer, E. L. , and Krogh, A. (1998). A hidden Markov model for predicting transmembrane helices in protein sequences. In J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. ), Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology. Vol. 6. : AAAI Press, pp. 175–182. , and Valencia, A. (1998). Automatic classification of proteins in functional classes using database annotations. CABIOS 14: 542–543. Tatusov, R. , Galperin, M. , Natale, D.

And Sherlock, G. (2000). Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genetics 25: 25–29. The authors describe the creation of a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, the Gene Ontology (GO) Consortium has constructed three independent ontologies: biological process, molecular function, and cellular component. The GO concept is intended to make possible, in a flexible and dynamic way, the annotation of homologous gene and protein sequences in multiple organisms, using a common vocabulary that results in the ability to query and retrieve genes and proteins based on their shared biology.

The ‘‘common annotation’’ approach can be used not only with pro- tein families but also with conditions aiming at a higher level in the protein family hierarchy. Only the annotation common to all members of this (for instance) superfamily will be copied over. Our methodology is independent of the multidomain organization of proteins. If a certain condition aims at a single domain that occurs with various other domains, it can be expected that only the annotation referring to this single domain will be found in all relevant characterized proteins.

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