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http://dx.doi.org/10.17703/JCCT.2019.5.3.339

Implementation and Application of Multiple Local Alignment  

Lee, Gye Sung (Dept. of Software, Dankook Univ)
Publication Information
The Journal of the Convergence on Culture Technology / v.5, no.3, 2019 , pp. 339-344 More about this Journal
Abstract
Global sequence alignment in search of similarity or homology favors larger size of the sequence because it keeps looking for more similar section between two sequences in the hope that it adds up scores for matched part in the rest of the sequence. If a substantial size of mismatched section exists in the middle of the sequence, it greatly reduces the total alignment score. In this case a whole sequence would be better to be divided into multiple sections. Overall alignment score over the multiple sections of the sequence would increase as compared to global alignment. This method is called multiple local alignment. In this paper, we implement a multiple local alignment algorithm, an extension of Smith-Waterman algorithm and show the experimental results for the algorithm that is able to search for sub-optimal sequence.
Keywords
Local Alignment; Smith-Waterman Algorithm; Multiple local alignment;
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