Prediction of E.Coli promoter gene sequences using a hybrid combination based on feature selection, fuzzy weighted pre-processing, and decision tree classifier

  • Authors:

  • Bayram Akdemir;Kemal Polat;Salih Günes

  • Affiliations:

  • Selcuk University, Dept. of Electrical & Electronics Engineering, Konya, Turkey;Selcuk University, Dept. of Electrical & Electronics Engineering, Konya, Turkey;Selcuk University, Dept. of Electrical & Electronics Engineering, Konya, Turkey

  • Venue:
  • KES'07/WIRN'07 Proceedings of the 11th international conference, KES 2007 and XVII Italian workshop on neural networks conference on Knowledge-based intelligent information and engineering systems: Part I
  • Year:
  • 2007

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Abstract

In this paper, we have investigated the real-world task of recognizing biological concepts in DNA sequences. Recognizing promoters in strings that represent nucleotides (one of A, G, T, or C) has been performed using a hybrid approach based on combining feature selection (FS), fuzzy weighted preprocessing, and C4.5 decision tree classifier (DCS). Dimensionality of E.coli Promoter Gene Sequences dataset has 57 attributes and 106 samples including 53 promoters and 53 non-promoters. The proposed approach consists of three stages. Firstly, we have used the FS process to reduce the dimensionality of E.coli Promoter Gene Sequences dataset that has 57 attributes. So the dimensionality of this dataset has been reduced to 4 attributes by means of FS process. Secondly, fuzzy weighted pre-processing has been used to weight E.coli Promoter Gene Sequences dataset that has 4 attributes in interval of [0,1]. Finally, C4.5 decision tree classifier algorithm has been run to estimation the E.coli Promoter Gene Sequences. In order to show the performance of the proposed system, we have used the predicton accuracy and 10-fold cross validation. 93.33% classification accuracy has been obtained by the proposed system using 10-fold cross validation. This success shows that the proposed system is a robust and effective system in the prediction of E.coli Promoter Gene Sequences.