Detection of Splice Sites Using Support Vector Machine

  • Pritish Varadwaj
  • Neetesh Purohit
  • Bhumika Arora
Part of the Communications in Computer and Information Science book series (CCIS, volume 40)

Abstract

Automatic identification and annotation of exon and intron region of gene, from DNA sequences has been an important research area in field of computational biology. Several approaches viz. Hidden Markov Model (HMM), Artificial Intelligence (AI) based machine learning and Digital Signal Processing (DSP) techniques have extensively and independently been used by various researchers to cater this challenging task. In this work, we propose a Support Vector Machine based kernel learning approach for detection of splice sites (the exon-intron boundary) in a gene. Electron-Ion Interaction Potential (EIIP) values of nucleotides have been used for mapping character sequences to corresponding numeric sequences. Radial Basis Function (RBF) SVM kernel is trained using EIIP numeric sequences. Furthermore this was tested on test gene dataset for detection of splice site by window (of 12 residues) shifting. Optimum values of window size, various important parameters of SVM kernel have been optimized for a better accuracy. Receiver Operating Characteristic (ROC) curves have been utilized for displaying the sensitivity rate of the classifier and results showed 94.82% accuracy for splice site detection on test dataset.

Keywords

Splice site Support vector machine Electron-ion interaction potential 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Pritish Varadwaj
    • 1
  • Neetesh Purohit
    • 1
  • Bhumika Arora
    • 1
  1. 1.Indian Institute of Information TechnologyAllahabad

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