Exon prediction on DNA-Gen Plasmodium falciparum by using Hidden Markov Model

Suhartati Agoes, Dadang Gunawan, Sar Sardy

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

Abstract

This paper will discuss about the exon prediction on DN A-Gen Plasmodium falciparum by using Hidden Markov Model (HMM). The increment of state number was done randomly up to 100, by using a backward-forward HMM with some transition and emission components on each state. Based on the Gen basic structure on coding sequence (CDS), it is developed four expansion models for increasing the state number. The Viterbi algorithm is used for training process, and Viterbi and Baum-Welch algorithms are used for testing process. The correlation coefficient (CC) is applied as a performance indicator for all expansion models. The result of simulation for the basic structure at state 9, show that the best average CC value is 0.73 for Viterbi algorithm, and is 0.72 for Baum-Welch algorithm. In the expansion models, it is found that the average CC value for second expansion model is 0.78 for both algorithms at stage 100. The average processing time for training is shorter at stage 20 and 30, but almost 12-15 times longer at stage 100, while the average processing time for testing by using Baum-Welch algorithm is twice longer than Viterbi algorithm.

Original languageEnglish
Title of host publicationCITSA 2007 - Int. Conference on Cybernetics and Information Technologies, Systems and Applications and CCCT 2007 - Int. Conference on Computing, Communications and Control Technologies, Proceedings
Pages66-69
Number of pages4
Publication statusPublished - 1 Dec 2007
Event4th International Conference on Cybernetics and Information Technologies, Systems and Applications, CITSA 2007, Jointly with the 5th International Conference on Computing, Communications and Control Technologies, CCCT 2007 - Orlando, FL, United States
Duration: 12 Jul 200715 Jul 2007

Publication series

NameCITSA 2007 - Int. Conference on Cybernetics and Information Technologies, Systems and Applications and CCCT 2007 - Int. Conference on Computing, Communications and Control Technologies, Proceedings
Volume1

Conference

Conference4th International Conference on Cybernetics and Information Technologies, Systems and Applications, CITSA 2007, Jointly with the 5th International Conference on Computing, Communications and Control Technologies, CCCT 2007
CountryUnited States
CityOrlando, FL
Period12/07/0715/07/07

Keywords

  • Exon prediction
  • HMM
  • Plasmodium falciparum

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  • Cite this

    Agoes, S., Gunawan, D., & Sardy, S. (2007). Exon prediction on DNA-Gen Plasmodium falciparum by using Hidden Markov Model. In CITSA 2007 - Int. Conference on Cybernetics and Information Technologies, Systems and Applications and CCCT 2007 - Int. Conference on Computing, Communications and Control Technologies, Proceedings (pp. 66-69). (CITSA 2007 - Int. Conference on Cybernetics and Information Technologies, Systems and Applications and CCCT 2007 - Int. Conference on Computing, Communications and Control Technologies, Proceedings; Vol. 1).