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HLAB27Pred: SVM-based precise method for predicting HLA-B*2705 binding peptides in antigenic sequences

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Abstract

Binding of Major histocompatibility complex (MHC) peptide is a prerequisite for T cell activation in the immune system. MHC-binding peptides have shown promising results for immunodiagnostics and immunotherapeutic purposes. HLA-B*2705 is found to be associated with the development of variety of autoimmune diseases including Ankylosing spondylitis. Detecting MHC class I allele HLA-B*2705 binding peptides can reduce the number of peptides that need to be tested experimentally. This work describes the implementation of SVM algorithm, developed for the identification of HLA-B*2705 binding peptides in antigenic sequences. The specificity and sensitivity obtained during the development of this server are 85 and 86 %, respectively. Whereas average precision and average recall values were observed to be 85 and 86 %, respectively. Training on wide-scale data made this method more accurate and robust than all available other methods for the HLA-B*2705 allele and would prove its usability in the biomedical domain. A web server HLA-B27pred is available at http://www.nuccore.org/hlab27pred for academic and research purpose.

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Acknowledgments

Authors would like to thank Sachin Pundhir, Digvijay Singh Chauhan, and Shekhar Chandra for technical help and discussions.

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Authors and Affiliations

  1. School of Bio-Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632 014, India

    Arun Gupta

  2. Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Council of Scientific and Industrial Research, Chattar Manzil Palace, PO Box 173, Lucknow, 22600, India

    Sharat Chandra

  3. Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Solan, HP, 173234, India

    Tiratha Raj Singh

Authors
  1. Arun Gupta
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  2. Sharat Chandra
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  3. Tiratha Raj Singh
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Corresponding author

Correspondence to Tiratha Raj Singh.

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A. Gupta and S. Chandra are joint first authors and equal contributors.

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Gupta, A., Chandra, S. & Singh, T.R. HLAB27Pred: SVM-based precise method for predicting HLA-B*2705 binding peptides in antigenic sequences. Netw Model Anal Health Inform Bioinforma 3, 56 (2014). https://doi.org/10.1007/s13721-014-0056-z

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  • DOI: https://doi.org/10.1007/s13721-014-0056-z

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