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A Novel Partial Sequence Alignment Tool for Finding Large Deletions
Joint Authors
Kursun, Olcay
Ustek, Duran
Aruk, Taner
Source
Issue
Vol. 2012, Issue 2012 (31 Dec. 2012), pp.1-6, 6 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2012-04-01
Country of Publication
Egypt
No. of Pages
6
Main Subjects
Natural & Life Sciences (Multidisciplinary)
Medicine
Information Technology and Computer Science
Abstract EN
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.
American Psychological Association (APA)
Aruk, Taner& Ustek, Duran& Kursun, Olcay. 2012. A Novel Partial Sequence Alignment Tool for Finding Large Deletions. The Scientific World Journal،Vol. 2012, no. 2012, pp.1-6.
https://search.emarefa.net/detail/BIM-491213
Modern Language Association (MLA)
Aruk, Taner…[et al.]. A Novel Partial Sequence Alignment Tool for Finding Large Deletions. The Scientific World Journal No. 2012 (2012), pp.1-6.
https://search.emarefa.net/detail/BIM-491213
American Medical Association (AMA)
Aruk, Taner& Ustek, Duran& Kursun, Olcay. A Novel Partial Sequence Alignment Tool for Finding Large Deletions. The Scientific World Journal. 2012. Vol. 2012, no. 2012, pp.1-6.
https://search.emarefa.net/detail/BIM-491213
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-491213