The identification of functional motifs in a DNA sequence is fundamentally a statistical pattern recognition problem. This paper introduces a new algorithm for the recognition of functional transcription start sites （TSSs） in human genome sequences, in which a RBF neural network is adopted, and an improved heuristic method for a 5-tuple feature viable construction, is proposed and implemented in two RBFPromoter and ImpRBFPromoter packages developed in Visual C＋＋ 6.0. The algorithm is evaluated on several different test sequence sets. Compared with several other promoter recognition programs, this algorithm is proved to be more flexible, with stronger learning ability and higher accuracy.
This brief paper reports a hybrid algorithm we developed recently to solve the global optimization problems of multimodal functions, by combining the advantages of two powerful population-based metaheuristics differential evolution （DE） and particle swarm optimization （PSO）. In the hybrid denoted by DEPSO, each individual in one generation chooses its evolution method, DE or PSO, in a statistical learning way. The choice depends on the relative success ratio of the two methods in a previous learning period. The proposed DEPSO is compared with its PSO and DE parents, two advanced DE variants one of which is suggested by the originators of DE, two advanced PSO variants one of which is acknowledged as a recent standard by PSO community, and also a previous DEPSO. Benchmark tests demonstrate that the DEPSO is more competent for the global optimization of multimodal functions due to its high optimization quality.
CHEN Jie1,2,XIN Bin1,2,PENG ZhiHong1,2 & PAN Feng1,2 1 School of Automatic Control,Beijing Institute of Technology,Beijing 100081,China
Because it is hard to search similar structure for low similarity unknown structure proteins directly from the Protein Data Bank （PDB） database, 3D-structure is modeled in this paper for secondary structure regular fragments （α-Helices, β-Strands） of such proteins by the protein secondary structure prediction software, the Basic Local Alignment Search Tool （BLAST） and the side chain construction software SCWRL3. First, the protein secondary structure prediction software is adopted to extract secondary structure fragments from the unknown structure proteins. Then, regular fragments are regulated by BLAST based on comparative modeling, providing main chain configurations. Finally, SCWRL3 is applied to assemble side chains for regular fragments, so that 3D-structure of regular fragments of low similarity unknown structure protein is obtained. Regular fragments of several neurotoxins are used for test. Simulation results show that the prediction errors are less than 0.06nm for regular fragments less than 10 amino acids, implying the simpleness and effectiveness of the proposed method.
