The local DNA conformation in the region of transcription factor binding sites, determined by context, is one of the factors underlying the specificity of DNA-protein interactions. Analysis of the local conformation of a set of functional DNA sequences may allow for determination of the conservative conformational and physicochemical parameters reflecting molecular mechanisms of interaction. The web resource SITECON is designed to detect conservative conformational and physicochemical properties in transcription factor binding sites, contains a knowledge base of conservative properties for >100 high-quality sample sites and allows for recognition of potential transcription factor binding sites based on conservative properties from both the knowledge base and the results of analysis of a sample proposed by a user. The resource SITECON is available at http://wwwmgs.bionet.nsc.ru/mgs/programs/sitecon/.
We consider the predictions provided by the inductive theories. For these theories predictions are performed by the Inductive Statistical (I-S) inferences. It was noted by Hempel that the IS inference is statistically ambiguous. To avoid this ambiguity we need to use the rules that satisfy the Requirement of Maximum Specificity (RMS). The formal definition of the RMS wasn't given by Hempel. We define the notions of law and probabilistic law, and also the sets of all laws L, and probabilistic laws LP. We prove that the set SPL of Strongest Probabilistic Laws (with the maximum values of conditional probability) contains the set L, so we have L ⊂ SPL ⊂ LP. We prove that the maximum specific rules-the strongest SPL rules for prediction of atoms-satisfy the RMS condition. The maximum specific rules may be used in IS inference. We prove that the set MSR of all Maximum Specific Rules is consistent and the IS inferences based on MSR rules avoid the problem of statistical ambiguity. We define Semantic Probabilistic Inferences (SP-inference) that infer the sets L, LP, SPL, MSR. Finally, we mention the program system 'Discovery', which realize the SP-inference and discovers the sets L, LP, SPL, MSR. This system was applied for solution of many practical tasks (see website www.math.nsc.ru/AP/ScientificDiscovery).
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