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Beyond Bioinformatics | |
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Title |
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An SVM method using evolutionary information for the identification of allergenic proteins
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Authors |
Kandaswamy Krishna Kumar1, *and Prakash Shrikrishna Shelokar1
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Affiliation |
1Insilico Consulting, 402, Citi Centre, 39/2 Erandwane, Karve Road, Pune-411004, Maharashtra, India
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biotechkk@gmail.com; * Corresponding author
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Article Type |
Prediction Model
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Date |
received December 28, 2007; revised January 17, 2008; accepted January 19, 2008; published January 27, 2008
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Abstract |
This study presents an allergenic protein prediction system that appears to be capable of producing high sensitivity and specificity. The proposed system is based on support vector machine (SVM) using evolutionary information in the form of an amino acid position specific scoring matrix (PSSM). The performance of this system is assessed by a 10-fold cross-validation experiment using a dataset consisting of 693 allergens and 1041 non-allergens obtained from Swiss-Prot and Structural Database of Allergenic Proteins (SDAP). The PSSM method produced an accuracy of 90.1% in comparison to the methods based on SVM using amino acid, dipeptide composition, pseudo (5-tier) amino acid composition that achieved an accuracy of 86.3, 86.5 and 82.1% respectively. The results show that evolutionary information can be useful to build more effective and efficient allergen prediction systems
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Keywords |
allergenic proteins; evolutionary information; PSSM; amino-acid composition; dipeptide composition; SVM
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Citation |
Kumar & Shelokar, Bioinformation 2(6): 253-256 (2008)
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Edited by |
P. Kangueane
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ISSN |
0973-2063
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Publisher |
Biomedical Informatics Publishing Group
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Copyright |
Publisher
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Copyright Transfer Agreement |
The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.
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License |
This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.
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