An enhanced algorithm for multiple sequence alignment of protein sequences using genetic algorithm

One of the most fundamental operations in biological sequence analysis is multiple sequence alignment (MSA). The basic of multiple sequence alignment problems is to determine the most biologically plausible alignments of protein or DNA sequences. In this paper, an alignment method using genetic algorithm for multiple sequence alignment has been proposed. Two different genetic operators mainly crossover and mutation were defined and implemented with the proposed method in order to know the population evolution and quality of the sequence aligned. The proposed method is assessed with protein benchmark dataset, e.g., BALIBASE, by comparing the obtained results to those obtained with other alignment algorithms, e.g., SAGA, RBT-GA, PRRP, HMMT, SBPIMA, CLUSTALX, CLUSTAL W, DIALIGN and PILEUP8 etc. Experiments on a wide range of data have shown that the proposed algorithm is much better (it terms of score) than previously proposed algorithms in its ability to achieve high alignment quality

High Performance Switched Reluctance Drives

PhD ThesisThe fully-pitched winding arrangement is one of the most radical changes in the design of doubly-salient reluctance motors in recent times. By replacing conventional shortpitched windings with fully-pitched windings, the resulting machine has a strong and position dependant mutual coupling between phases. The major torque producing mechanism is due to changes in mutual inductance with rotor position. This enables the windings to be better utilised, and with correct selection of excitation all phases can contribute useful torque all of the time. The increased winding utilisation requires a lower MMF per phase in comparison with a short-pitch wound machine with a single phase excited. Given a suitable winding configuration and machine dimensions, the copper losses for a given torque can be significantly lower than an equivalent conventional switched reluctance machine. Operation of a three phase fully-pitched winding switched reluctance machine has been studied theoretically, in simulation and experimentally. The experimental drive comprises of a D132 frame 12:8 machine, IGBT power converter and DSP controller. Operation with unipolar phase currents has been investigated over a wide speed range and performance compared with a conventional switched reluctance machine. Bipolar operation with several different excitation patterns has been investigated. Unipolar operation gives the largest torque/speed envelope with a simple controller, although bipolar modes can equal this with a more complex controller. Results show that for equal RMS phase current the average torque produced by four different modes of excitation are approximately equal. However, there is a large difference in the torque ripple and acoustic noise performance of each mode. Current control in switched reluctance machines is complicated by the non-linear nature of the load. By controlling flux-linkage rather than current a linear load model can be used. A discrete time 'dead-beat' flux-linkage controller has been implemented which gives superior phase current control performance to other types of controller with the same sample interval. A new method of constant torque operation based on 'flux ramps' has been proposed. This method gives predictable performance and enables constant torque operation over a wide speed range. A Genetic Algorithm has been shown to be very effective when applied to the problem of optimising the 'flux ramps' for minimum torque ripple. A speed controller has been implemented which makes use of the Genetic Algorithm optimised flux ramps to give smooth torque over a wide speed range.Royal Societ