724 research outputs found
CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources
International audienceBACKGROUND: The functions of proteins are strongly related to their localization in cell compartments (for example the cytoplasm or membranes) but the experimental determination of the sub-cellular localization of proteomes is laborious and expensive. A fast and low-cost alternative approach is in silico prediction, based on features of the protein primary sequences. However, biologists are confronted with a very large number of computational tools that use different methods that address various localization features with diverse specificities and sensitivities. As a result, exploiting these computer resources to predict protein localization accurately involves querying all tools and comparing every prediction output; this is a painstaking task. Therefore, we developed a comprehensive database, called CoBaltDB, that gathers all prediction outputs concerning complete prokaryotic proteomes. DESCRIPTION: The current version of CoBaltDB integrates the results of 43 localization predictors for 784 complete bacterial and archaeal proteomes (2.548.292 proteins in total). CoBaltDB supplies a simple user-friendly interface for retrieving and exploring relevant information about predicted features (such as signal peptide cleavage sites and transmembrane segments). Data are organized into three work-sets ("specialized tools", "meta-tools" and "additional tools"). The database can be queried using the organism name, a locus tag or a list of locus tags and may be browsed using numerous graphical and text displays. CONCLUSIONS: With its new functionalities, CoBaltDB is a novel powerful platform that provides easy access to the results of multiple localization tools and support for predicting prokaryotic protein localizations with higher confidence than previously possible. CoBaltDB is available at http://www.umr6026.univ-rennes1.fr/english/home/research/basic/software/cobalten
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Automatic design of analogue circuits
This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Evolvable Hardware (EHW) is a promising area in electronics today. Evolutionary Algorithms (EA), together with a circuit simulation tool or real hardware, automatically designs a circuit for a given problem. The circuits evolved may have unconventional designs and be less dependent on the personal knowledge of a designer. Nowadays, EA are represented by Genetic Algorithms (GA), Genetic Programming (GP) and Evolutionary Strategy (ES). While GA is definitely the most popular tool, GP has rapidly developed in recent years and is notable by its outstanding results. However, to date the use of ES for analogue circuit synthesis has been limited to a few applications.
This work is devoted to exploring the potential of ES to create novel analogue designs. The narrative of the thesis starts with a framework of an ES-based system generating simple circuits, such as low pass filters. Then it continues with a step-by-step progression to increasingly sophisticated designs that require additional strength from the system. Finally, it describes the modernization of the system using novel techniques that enable the synthesis of complex multi-pin circuits that are newly evolved.
It has been discovered that ES has strong power to synthesize analogue circuits. The circuits evolved in the first part of the thesis exceed similar results made previously using other techniques in a component economy, in the better functioning of the evolved circuits and in the computing power spent to reach the results. The target circuits for evolution in the second half are chosen by the author to challenge the capability of the developed system. By functioning, they do not belong to the conventional analogue domain but to applications that are usually adopted by digital circuits. To solve the design tasks, the system has been gradually developed to support the ability of evolving increasingly complex circuits.
As a final result, a state-of-the-art ES-based system has been developed that possesses a novel mutation paradigm, with an ability to create, store and reuse substructures, to adapt the mutation, selection parameters and population size, utilize automatic incremental evolution and use the power of parallel computing. It has been discovered that with the ability to synthesis the most up-to-date multi-pin complex analogue circuits that have ever been automatically synthesized before, the system is capable of synthesizing circuits that are problematic for conventional design with application domains that lay beyond the conventional application domain for analogue circuits
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