References of "OUZOUNIS, C"
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See detailSequence analysis of the Methanococcus jannaschii genome and the prediction of protein function
Andrade, M.; Casari, G.; deDaruvar, A. et al

in Computer Applications in the Biosciences [=CABIOS] (1997), 13(4), 481-483

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See detailEXPLORING THE MYCOPLASMA-CAPRICOLUM GENOME - A MINIMAL CELL REVEALS ITS PHYSIOLOGY
BORK, P.; OUZOUNIS, C.; CASARI, G. et al

in Molecular Microbiology (1995), 16(5), 955-967

We report on the analysis of 214 kb of the parasitic eubacterium Mycoplasma capricolum sequenced by genomic walking techniques. The 287 putative proteins detected to date represent about half of the ... [more ▼]

We report on the analysis of 214 kb of the parasitic eubacterium Mycoplasma capricolum sequenced by genomic walking techniques. The 287 putative proteins detected to date represent about half of the estimated total number of 500 predicted for this organism. A large fraction of these (75%) can be assigned a likely function as a result of similarity searches. Several important features of the functional organization of this small genome are already apparent. Among these are (i) the expected relatively large number of enzymes involved in metabolic transport and activation, for efficient use of host cell nutrients; (ii) the presence of anabolic enzymes; (iii) the unexpected diversity of enzymes involved in DNA replication and repair; and (iv) a sizeable number of orthologues (82 so far) in Escherichia coil. This survey is beginning to provide a detailed view of how M. capricolum manages to maintain essential cellular processes with a genome much smaller than that of its bacterial relatives. [less ▲]

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See detailCHALLENGING TIMES FOR BIOINFORMATICS
CASARI, G.; ANDRADE, M. A.; BORK, P. et al

in Nature (1995), 376(6542), 647-648

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See detailGeneQuiz: a workbench for sequence analysis
Scharf, M.; Schneider, Reinhard UL; Casari, G. et al

in Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, ISMB-94 (1994)

We present the prototype of a software system, called GeneQuiz, for large-scale biological sequence analysis. The system was designed to meet the needs that arise in computational sequence analysis and ... [more ▼]

We present the prototype of a software system, called GeneQuiz, for large-scale biological sequence analysis. The system was designed to meet the needs that arise in computational sequence analysis and our past experience with the analysis of 171 protein sequences of yeast chromosome III. We explain the cognitive challenges associated with this particular research activity and present our model of the sequence analysis process. The prototype system consists of two parts: (i) the database update and search system (driven by perl programs and rdb, a simple relational database engine also written in perl) and (ii) the visualization and browsing system (developed under C++/ET++). The principal design requirement for the first part was the complete automation of all repetitive actions: database updates, efficient sequence similarity searches and sampling of results in a uniform fashion. The user is then presented with "hit-lists" that summarize the results from heterogeneous database searches. The expert's primary task now simply becomes the further analysis of the candidate entries, where the problem is to extract adequate information about functional characteristics of the query protein rapidly. This second task is tremendously accelerated by a simple combination of the heterogeneous output into uniform relational tables and the provision of browsing mechanisms that give access to database records, sequence entries and alignment views. Indexing of molecular sequence databases provides fast retrieval of individual entries with the use of unique identifiers as well as browsing through databases using pre-existing cross-references. The presentation here covers an overview of the architecture of the system prototype and our experiences on its applicability in sequence analysis. [less ▲]

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See detailPREDICTION OF PROTEIN-STRUCTURE BY EVALUATION OF SEQUENCE-STRUCTURE FITNESS - ALIGNING SEQUENCES TO CONTACT PROFILES DERIVED FROM 3-DIMENSIONAL STRUCTURES
OUZOUNIS, C.; SANDER, C.; SCHARF, M. et al

in Journal of Molecular Biology (1993), 232(3), 805-825

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See detailCOMPREHENSIVE SEQUENCE-ANALYSIS OF THE 182 PREDICTED OPEN READING FRAMES OF YEAST CHROMOSOME-III
BORK, P.; OUZOUNIS, C.; SANDER, C. et al

in Protein Science : A Publication of the Protein Society (1992), 1(12), 1677-1690

With the completion of the first phase of the European yeast genome sequencing project, the complete DNA sequence of chromosome III of Saccharomyces cerevisiae has become available (Oliver, S.G., et al ... [more ▼]

With the completion of the first phase of the European yeast genome sequencing project, the complete DNA sequence of chromosome III of Saccharomyces cerevisiae has become available (Oliver, S.G., et al., 1992, Nature 357, 38-46). We have tested the predictive power of computer sequence analysis on the 176 probable protein products of this chromosome, after exclusion of six problem cases. When the results of database similarity searches are pooled with prior knowledge, a likely function can be assigned to 42% of the proteins, and a predicted three-dimensional structure to a third of these (140% of the total). The function of the remaining 58% remains to be determined. Of these, about one-third have one or more probable transmembrane segments. Among the most interesting proteins with predicted functions are a new member of the type X polymerase family, a transcription factor with an N-terminal DNA-binding domain related to GAL4, a ''fork head'' DNA-binding domain previously known only in Drosophila and in mammals, and a putative methyltransferase. Our analysis increased the number of known significant sequence similarities on chromosome III by 13, to now 67. Although the near 40% success rate of identifying unknown protein function by sequence analysis is surprisingly high, the information gap between known protein sequences and unknown function is expected to widen and become a major bottleneck of genome projects in the near future. Based on the experience gained in this test study, we suggest that the development of an automated computer workbench for protein sequence analysis must be an important item in genome projects. [less ▲]

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See detailWHATS IN A GENOME
BORK, P.; OUZOUNIS, C.; SANDER, C. et al

in Nature (1992), 358(6384), 287-287

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