A prototype for multiple whole genome alignment

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

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 languageEnglish (US)
Title of host publicationProceedings of the 36th Annual Hawaii International Conference on System Sciences, HICSS 2003
EditorsRalph H. Sprague
PublisherInstitute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)0769518745, 9780769518749
DOIs
StatePublished - Jan 1 2003
Event36th Annual Hawaii International Conference on System Sciences, HICSS 2003 - Big Island, United States
Duration: Jan 6 2003Jan 9 2003

Publication series

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

Other

Other36th Annual Hawaii International Conference on System Sciences, HICSS 2003
CountryUnited States
CityBig Island
Period1/6/031/9/03

Fingerprint

Genes
Microorganisms
Decomposition

ASJC Scopus subject areas

  • Information Systems
  • Computer Science Applications

Cite this

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 [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; Benson, A.

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 proceedingConference 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). https://doi.org/10.1109/HICSS.2003.1174803
Deogun, J. S. ; Ma, Fangrui ; Yang, Jingyi ; Benson, A. / 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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