A New Heuristic Approach for DNA Sequences Alignment

Abstract

The problem of comparing DNA sequences is one of the most significant tasks in the field of computational biology. It helps locating the similarities and differences between pairs of DNA sequences. This task can be achieved by finding the longest common substrings between DNA sequences and consequently aligning them. The complexity of this task is due to the high computational power and huge space consuming. Comparing DNA sequences leads to infer the cause of a certain disease beside many significant biological applications. This paper introduces a new Heuristic Approach for DNA Sequences Alignment between two DNA sequences. The new approach is based on three processing phases: the first phase finds the multiple common substrings in the two sequences, the second one sorts the obtained common substrings descending according to their lengths, and the last phase generates the optimal two aligned sequences. The modules of the new approach have been implemented and tested in C# language under Windows platform. The obtained results manifest a reduction in both time of processing and memory requirements.