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A survey and improvement on Protein Sequence Alignment using Evolutionary Algorithms

Narimani, Zahra | 2009

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  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 40152 (19)
  4. University: Sharif University of Technology
  5. Department: Computer Engineering
  6. Advisor(s): Abolhassani, Hassan
  7. Abstract:
  8. Protein multiple sequence alignment is one of important problems in biology which no polynomial time algorithms is known for it yet. Due to importance of this problem, several methods have been developed to find an approximate solution for it. Approximation algorithms, Evolutionary algorithms and Probabilistic methods are some of these methods. According to evolutionary nature of this problem, evolutionary algorithms and specifically genetic algorithms can be a potential good solution method for this problem. In this project we have a survey on using genetic algorithms for this problem and after mentioning benefits and draw backs of existing methods, we develop a method for improving one of studied efficient algorithms. At the end by introducing a new way for population initialization and a new operation, we develop our own algorithm for this problem. Our solution is not only precise in contrast to other methods, but its running time is also improved impressively. This reduction in running time is the result of using simple operators and also a reduction in number of genetic generations in a single run. The new algorithm is implemented in java and the result is tested using BAliBASE2.01, which is a set of human and semi automate made multiple sequence alignments. This dataset is created according to biological information and is not biased toward a specific method, so it can be a good test set. Finally our result is compared to two of the recent genetic algorithms in this area. This represents improvement of precision and running time in the new method
  9. Keywords:
  10. Evolutionary Algorithm ; Genetic Algorithm ; Multiple Sequence Aliqument ; Substitution Matrix

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