A prototype for multiple whole genome alignment

J. S. Deogun; Fangrui Ma; Jingyi Yang; A. Benson

doi:10.1109/HICSS.2003.1174803

A prototype for multiple whole genome alignment

J. S. Deogun, Fangrui Ma, Jingyi Yang, A. Benson

Food Science and Technology

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

2 Scopus citations

Abstract

In this paper, we briefly describe a prototype of the software system we have developed for multiple whole genome alignment. To develop our algorithm, we have to solve several problems including decomposition of genomes with a suffix tree, finding an LIS for multiple MUM sequences, and iterative pairwise multiple sequence alignment. This results in an overall linear time complexity for our algorithm for finding conserved regions; and between linear and quadratic time complexity for multiple whole genome alignment. One application is the problem of finding a maximum set of conserved regions in closely related microorganisms.

Original language	English (US)
Title of host publication	Proceedings of the 36th Annual Hawaii International Conference on System Sciences, HICSS 2003
Editors	Ralph H. Sprague
Publisher	Institute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)	0769518745, 9780769518749
DOIs	https://doi.org/10.1109/HICSS.2003.1174803
State	Published - 2003
Event	36th Annual Hawaii International Conference on System Sciences, HICSS 2003 - Big Island, United States Duration: Jan 6 2003 → Jan 9 2003

Publication series

Name	Proceedings of the 36th Annual Hawaii International Conference on System Sciences, HICSS 2003

Other

Other	36th Annual Hawaii International Conference on System Sciences, HICSS 2003
Country/Territory	United States
City	Big Island
Period	1/6/03 → 1/9/03

ASJC Scopus subject areas

Information Systems
Computer Science Applications

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10.1109/HICSS.2003.1174803

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Deogun, J. S., Ma, F., Yang, J., & Benson, A. (2003). A prototype for multiple whole genome alignment. In R. H. Sprague (Ed.), Proceedings of the 36th Annual Hawaii International Conference on System Sciences, HICSS 2003 Article 1174803 (Proceedings of the 36th Annual Hawaii International Conference on System Sciences, HICSS 2003). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/HICSS.2003.1174803

A prototype for multiple whole genome alignment. / Deogun, J. S.; Ma, Fangrui; Yang, Jingyi et al.
Proceedings of the 36th Annual Hawaii International Conference on System Sciences, HICSS 2003. ed. / Ralph H. Sprague. Institute of Electrical and Electronics Engineers Inc., 2003. 1174803 (Proceedings of the 36th Annual Hawaii International Conference on System Sciences, HICSS 2003).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Deogun, JS, Ma, F, Yang, J & Benson, A 2003, A prototype for multiple whole genome alignment. in RH Sprague (ed.), Proceedings of the 36th Annual Hawaii International Conference on System Sciences, HICSS 2003., 1174803, Proceedings of the 36th Annual Hawaii International Conference on System Sciences, HICSS 2003, Institute of Electrical and Electronics Engineers Inc., 36th Annual Hawaii International Conference on System Sciences, HICSS 2003, Big Island, United States, 1/6/03. https://doi.org/10.1109/HICSS.2003.1174803

Deogun JS, Ma F, Yang J, Benson A. A prototype for multiple whole genome alignment. In Sprague RH, editor, Proceedings of the 36th Annual Hawaii International Conference on System Sciences, HICSS 2003. Institute of Electrical and Electronics Engineers Inc. 2003. 1174803. (Proceedings of the 36th Annual Hawaii International Conference on System Sciences, HICSS 2003). doi: 10.1109/HICSS.2003.1174803

Deogun, J. S. ; Ma, Fangrui ; Yang, Jingyi et al. / A prototype for multiple whole genome alignment. Proceedings of the 36th Annual Hawaii International Conference on System Sciences, HICSS 2003. editor / Ralph H. Sprague. Institute of Electrical and Electronics Engineers Inc., 2003. (Proceedings of the 36th Annual Hawaii International Conference on System Sciences, HICSS 2003).

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author = "Deogun, {J. S.} and Fangrui Ma and Jingyi Yang and A. Benson",

note = "Funding Information: This research was supported in part by NSF EPSCOR Grant No. EPS-0091900 and NSF Digital Government Grant No. EIA-0091530. Publisher Copyright: {\textcopyright} 2003 IEEE.; 36th Annual Hawaii International Conference on System Sciences, HICSS 2003 ; Conference date: 06-01-2003 Through 09-01-2003",

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A prototype for multiple whole genome alignment

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