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Articles by Biswajit Sahoo
Total Records ( 2 ) for Biswajit Sahoo
  Satarupa Mohanty and Biswajit Sahoo
  Motif search in computational biology is a most challenging problem. This plays a crucial role in gene finding and understanding the gene regulation relationship. In this study, a new efficient algorithm is proposed for the (l, d) motif search problem to find all string of length l which present in each of the input string with d mismatches. The method is based on 2 key aspects. First, a group of 3 l-mers of close proximity is processed efficaciously to generate the common d-neighborhood and second the data structure bit vector is used which simplifies the process of making the union and intersection of the common d-neighborhood. The proposed approach can be considered to be a hybrid one, as it integrates the existing algorithm with the novel ideas of common d-neighborhood generation to achieve better running time. Moreover, a parallel version of proposed method is also presented which runs on 4 SMP cluster systems with each of 2.4 GHz Intel Pentium-IV having 16 GB ram running under Red Hat Linux. The experimental result shows that the proposed algorithm is linearly scalable with the number of processors.
  Satarupa Mohanty , Rohan Chauhan and Biswajit Sahoo
  Analysis of motif in DNA sequences are growing into a significant context in the domain of gene regulation and in the same way, identification of motif is a most crucial issue in the study of computational biology. This study addresses the issues of motif search in biological DNA sequences using an evolutionary approach. The experiment is conducted using the Genetic algorithm framework along with a novel approach of generation of a highly fit population of solutions and then converging to optimal motif using secondary fitness function. The proposed model calculate the average value of given sequences and then iterate to generate the optimum population as the strings those are closer to the average value in order to achieve a better rate of convergence to the optimum motif. The experimental study on simulated data using evolutionary approach is recorded and proofs its consistency.
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