The BioTools Suite is a set of three comprehensive, platform-independent software packages (PepTool, GeneTool, and ChromaTool) developed for sequence assembly and analysis. In addition to supporting a large number of standard bioinformatics functions, these programs also incorporate a number of useful innovations including uniform graphical-user interface (GUI) design, direct internet connectivity, a novel approach to feature annotation, and a variety of enhanced algorithms for large scale proteome and genome analysis. This article describes the key features, recent changes, and general operation of all three programs.
Previous studies in data mining have yielded efficient algorithms for discovering association rules. To increase the expressiveness and relevance of the discovered rules, researche~s typically augment the thresholds with domain-specific knowledge. Most existing proposals use the relational approach to organize and maintain these multi-level concept hierarchies. We argue that an object-oriented approach is better suited for focusing the search and regulating the mining of association rules both at multi-levels within one concept hierarchy, and across multiple concept hierarchies. We propose an adaptive encodhtg scheme for focusing the mining on semantically deeper and more informative knowledge.We demonstrate that the application of an object-oriented approach provides us with the benefits of a flexible combination of multiple multi-level concept hierarchies for focusing the mining on more informative and refined knowledge, and also allows us to enjoy seamless integration of multi-level concept hierarchies with legacy databases. In addition, by using an adaptive encoding scheme, efficient algorithms developed for discovering association rules can be integrated into the object-oriented framework with no or little extm cost.
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