International Journal of Engineering Research in Computer Science and Engineering (IJERCSE)

The Prediction of Secondary Structure Protein Using Neural Networks and Support Vector Machine

Author : Sunnit Kaur ¹ Er. Navneet Bawa ²

Date of Publication :7th August 2016

Abstract: Precise prediction of protein secondary structure from the associated amino acids sequence is of great importance and also challenging task .Protein is an important molecule that performs a wide range of functions in biological system. The secondary structure of protein plays a key role in designing of drugs. Various tools are used for the secondary structure prediction of proteins such as Support vector machine and neural network, fuzzy logic. NN is machine learning methodology in which the network is trained using the recognized data sets.SVM is a supervised machine learning method is based on principle of the structural risk minimization. In this paper, both SVM and NN techniques are compared. For each NN and SVM, classifiers classifies the sequence in the 3-Level subclasses: Helix (H),Sheet(E)and coil(c).The objective is to acquire the maximum predict IVE accuracy with the minimal zed error. From the comparative study of SVM and NN it is concluded that technique takes lesser time than SVM

Reference :

1. Ibrahim Darwish1, Amr Radi2, Salah El-Bakry3 and ElSayed M. El-Sayed4 (2015) “Protein Secondary Structure Prediction Using Artificial Neural Network Implemented on FPGA”, International Journal of Bio-Medical Informatics and e-Health Volume 3, No.1, January - February 2015
2. Hanna Hendy, Weal Khaliah, Mohamed Rushdie, (2015) “A Study Of Intelligent Techniques for Protein Secondary Structure Prediction “International Journal "Information Models and Analyses" Volume 4, Number 1, 2015
3. Pradeep Singh ,Prof Rajbir Singh, et.al.(2015) “Improved Protein Function Classification Using Support Vector Machine “International Journal of Computer Science and Information Technologies, Vol. 6 (2) , 2015, 964-968.
4. Shavian Agarwal, et.al. (2014) “Prediction of Secondary Structure of Protein using Support Vector Machine “International Journal of Computer Applications® (IJCA) (0975 – 8887)
5. Annulet Kaur Johal, Prof. Rajbir Singh (2014)” Protein Secondary Structure Prediction Using Improved Support Vector Machine and Neural Networks”International Journal of Engineering and Computer Science ISSN: 2319- 7242 Volume 3 Issue 1, January 2014 Page No. 3593-3597
6. Patel Mauri Dinuba, Dr.Hitesh B Shah (2013)” Comparative Study of Multi-class Protein Structure Prediction Using Advanced Soft computing Techniques”International Journal of Engineering Science and Innovative Technology (IJESIT) Volume 2, Issue 2, March 2013
7. Shusha Shankar Ray and Shankar K. Pal (2013)” RNA Secondary Structure Prediction Using Soft Computing” IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 10, NO. 1,
8. Anil Kumar Mandle1, Pranitha Jain2, and Shailendra Kumar Srivastava (2012)”Protein Structure Prediction Using Support Vector Machine”International Journal on Soft Computing (IJSC) Vol.3, No.1,
9. FeeXia, Dou Y. ET. Al (2011) “FPGA accelerator for protein secondary structure prediction based on the GOR algorithm”, BMC Bioinformatics 12(Supple 1):S5.
10. Kaur RK, Kaur M, Kaur A. (2010) “Using Cluster Analysis for Protein Secondary Structure Prediction”, International Journal of Computer Applications (0975 – 8887) Vol. 4(12)
11. Kumar B, Jani NN (2010) “Prediction of Protein Secondary Structure based on GOR Algorithm Integrating with Multiple Sequences Alignment” , International Journal of Advanced Engineering & Applications.
12. Rao P.V.N, et.al (2010)“Protein Secondary Structure Prediction using Pattern Recognition Neural Network”, International Journal of Engineering Science and Technology Vol. 2(6), pp. 1752-1757
13. Singh R, Diol SK, Sandhu PS (2010) “Chou-Farman Method for Protein Structure Prediction using Cluster Analysis”, World Academy of Science, Engineering and Technology 72.
1. Ibrahim Darwish1, Amr Radi2, Salah El-Bakry3 and ElSayed M. El-Sayed4 (2015) “Protein Secondary Structure Prediction Using Artificial Neural Network Implemented on FPGA”, International Journal of Bio-Medical Informatics and e-Health Volume 3, No.1, January - February 2015
2. Hanna Hendy, Weal Khaliah, Mohamed Rushdie, (2015) “A Study Of Intelligent Techniques for Protein Secondary Structure Prediction “International Journal "Information Models and Analyses" Volume 4, Number 1, 2015
3. Pradeep Singh ,Prof Rajbir Singh, et.al.(2015) “Improved Protein Function Classification Using Support Vector Machine “International Journal of Computer Science and Information Technologies, Vol. 6 (2) , 2015, 964-968.
4. Shavian Agarwal, et.al. (2014) “Prediction of Secondary Structure of Protein using Support Vector Machine “International Journal of Computer Applications® (IJCA) (0975 – 8887)
5. .Annulet Kaur Johal, Prof. Rajbir Singh (2014)” Protein Secondary Structure Prediction Using Improved Support Vector Machine and Neural Networks”International Journal of Engineering and Computer Science ISSN: 2319- 7242 Volume 3 Issue 1, January 2014 Page No. 3593-3597
6. Patel Mauri Dinuba, Dr.Hitesh B Shah (2013)” Comparative Study of Multi-class Protein Structure Prediction Using Advanced Soft computing Techniques”International Journal of Engineering Science and Innovative Technology (IJESIT) Volume 2, Issue 2, March 2013
7. Shusha Shankar Ray and Shankar K. Pal (2013)” RNA Secondary Structure Prediction Using Soft Computing” IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 10, NO. 1,
8. Anil Kumar Mandle1, Pranitha Jain2, and Shailendra Kumar Srivastava (2012)”Protein Structure Prediction Using Support Vector Machine”International Journal on Soft Computing (IJSC) Vol.3, No.1,
9. FeeXia, Dou Y. ET. Al (2011) “FPGA accelerator for protein secondary structure prediction based on the GOR algorithm”, BMC Bioinformatics 12(Supple 1):S5.
10. Kaur RK, Kaur M, Kaur A. (2010) “Using Cluster Analysis for Protein Secondary Structure Prediction”, International Journal of Computer Applications (0975 – 8887) Vol. 4(12).
11. Kumar B, Jani NN (2010) “Prediction of Protein Secondary Structure based on GOR Algorithm Integrating with Multiple Sequences Alignment” , International Journal of Advanced Engineering & Applications.
12. Rao P.V.N, et.al (2010)“Protein Secondary Structure Prediction using Pattern Recognition Neural Network”, International Journal of Enginee
13. Singh R, Diol SK, Sandhu PS (2010) “Chou-Farman Method for Protein Structure Prediction using Cluster Analysis”, World Academy of Science, Engineering and Technology 72.