Applications of EMAGEN on comparing multiple prokaryotic genomes

Jitender S Deogun, Jingyi Yang, Fangrui Ma

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

Abstract

Comparing and aligning multiple genomes can produce valuable information regarding the species revolution. EMAGEN is an efficient algorithm to compare and align closely related multiple whole genomes. It aligns multiple whole genomes by first finding globally optimal consistent conserved regions among multiple genomes, then generating detailed alignment of the gaps between consecutive conserved regions with Clustal W. It uses two methods to find the globally optimal consistent conserved regions: Direct Matching and Functional Matching. DM method is to align genomes directly with their DNA sequences. FM method is used especially to align multiple prokaryotic genomes with their concatenated protein sequences. In this paper, We apply both methods of EMAGEN to prokaryotic genomes. Various experiments are performed with EMAGEN and their results are displayed and discussed. The results show that EMAGEN performs very well in the experiments and is very useful to compare different prokaryotic genomes.

Original languageEnglish (US)
Title of host publicationProceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04
EditorsF. Valafar, H. Valafar
Pages256-262
Number of pages7
StatePublished - Dec 1 2004
EventProceedings of the International Conference on Mathematics and Engineering Techniques in medicine and Biological Sciences, METMBS'04 - Las Vegas, NV, United States
Duration: Jun 21 2004Jun 24 2004

Publication series

NameProceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04

Conference

ConferenceProceedings of the International Conference on Mathematics and Engineering Techniques in medicine and Biological Sciences, METMBS'04
CountryUnited States
CityLas Vegas, NV
Period6/21/046/24/04

Fingerprint

Genes
DNA sequences
Experiments
Proteins

Keywords

  • Anchors
  • Multiple Whole Genome Alignment
  • Prokaryotic Genomes
  • Suffix Arrays

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Deogun, J. S., Yang, J., & Ma, F. (2004). Applications of EMAGEN on comparing multiple prokaryotic genomes. In F. Valafar, & H. Valafar (Eds.), Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04 (pp. 256-262). (Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04).

Applications of EMAGEN on comparing multiple prokaryotic genomes. / Deogun, Jitender S; Yang, Jingyi; Ma, Fangrui.

Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04. ed. / F. Valafar; H. Valafar. 2004. p. 256-262 (Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04).

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

Deogun, JS, Yang, J & Ma, F 2004, Applications of EMAGEN on comparing multiple prokaryotic genomes. in F Valafar & H Valafar (eds), Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04. Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04, pp. 256-262, Proceedings of the International Conference on Mathematics and Engineering Techniques in medicine and Biological Sciences, METMBS'04, Las Vegas, NV, United States, 6/21/04.
Deogun JS, Yang J, Ma F. Applications of EMAGEN on comparing multiple prokaryotic genomes. In Valafar F, Valafar H, editors, Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04. 2004. p. 256-262. (Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04).
Deogun, Jitender S ; Yang, Jingyi ; Ma, Fangrui. / Applications of EMAGEN on comparing multiple prokaryotic genomes. Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04. editor / F. Valafar ; H. Valafar. 2004. pp. 256-262 (Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04).
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