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The Scientific World JournalVolume 2012 2012, Article ID 694813, 6 pages

Research Article

Scientific and Technological Research Council of Turkey TUBITAK, 41470 Kocaeli, Turkey

Genetics Department, Institute for Experimental Medicine, Istanbul University, 34093 Istanbul, Turkey

Computer Engineering Department, Istanbul University, 34320 Istanbul, Turkey

Received 31 October 2011; Accepted 4 December 2011

Academic Editors: M. L. Bauman, S. Mastana, and D. E. Wells

Copyright © 2012 Taner Aruk et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Finding large deletions in genome sequences has become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Although there are a number of publically available next generation sequencing mapping and sequence alignment programs, these software packages do not correctly align fragments containing deletions larger than one kb. We present a fast alignment software package, BinaryPartialAlign, that can be used by wet lab scientists to find long structural variations in their experiments. For BinaryPartialAlign, we make use of the Smith-Waterman SW algorithm with a binary-search-based approach for alignment with large gaps that we called partial alignment. BinaryPartialAlign implementation is compared with other straight-forward applications of SW. Simulation results on mtDNA fragments demonstrate the effectiveness runtime and accuracy of the proposed method.





Author: Taner Aruk, Duran Ustek, and Olcay Kursun

Source: https://www.hindawi.com/



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