Bibliography | Grieb, Melanie: Synthetische Biologie - Automatische Familienklassifikation von Proteinen. University of Stuttgart, Faculty of Computer Science, Electrical Engineering, and Information Technology, Diploma Thesis No. 2311 (2005). 59 pages, english.
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CR-Schema | J.3 (Life and Medical Sciences)
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Keywords | ANACIN; bioinformatics; bioinformatik; protein; synthetic biology; synthetische biologie; sequenz; sequence; datenbanken; databases; model |
Abstract | It is expensive to experimentally determine the sequence, structure and function dependencies of a protein. Therefore, information is transferred from known to unknown proteins using the recognition of similar protein characteristics. Due to the decreasing cost of protein synthesis (currently 1.5$ per nucleotide, 0.1$ per nucleotide in the near future), the future goal is to use this knowledge to completely predict the function of a specific protein sequence for a non-experimental de novo design of proteins. Family classification plays a key role in finding the solution to that problem. Similarities in fold but not sequence are less likely to reveal common function than sequence similarity, which generally infers common structure. The family classification approach used by protein family databases is based on sequence similarity. Our research is based on the different approach of classifying proteins in families using amino acid annotations. In previous work, the transfer of annotations to different sequences in a protein family and the family classification were done manually. The duration of manual analysis was 3 months per database. In this thesis ANACIN, a software which automates annotation transfer and family classification, was created. With this software, the annotation accuracy could be improved compared to manual annotation. The analysis of the results of automated protein family classification led to the discovery of new protein families. The time for complete analysis was reduced to two days of computation and one day for the manual interpretation of the results.
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Full text and other links | PDF (1147113 Bytes) TAR-Archiv (153600 Bytes) Institut für technische Biochemie Access to students' publications restricted to the faculty due to current privacy regulations |
Contact | Email an melanie@melaniegrieb.de |
Department(s) | University of Stuttgart, Institute of Parallel and Distributed Systems, Simulation of Large Systems
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Project(s) | Synthetische Biologie (Institut für technische Biochemie)
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Entry date | August 28, 2005 |
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