Repeat Analysis in DNA Sequences with Parallel Computing Method on Grid

A. Arefin, A.I. Anwar, and A. Wasif (Bangladesh)


Grid, Alchemi, DNA, Repeated Patterns, Partitioning.


The development of Grid environment provides an efficient way for implementing the parallel algorithm. Here we focus on the discovery of short recurring patterns in DNA sequences that represent binding sites for certain proteins in the process of gene regulation. We develop parallel computing algorithm for solving this problem by partitioning the overall DNA sequences. This provides us an option to implement the algorithm on Grid and to evaluate its performance. We use the open source software “Alchemi” for building the Grid environment. Also by using a merging repeat approach to find these patterns, we address other related problems, including finding of repetition with insertion and deletion.

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