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IAPR International Conference on Pattern Recognition in Bioinformatics

PRIB 2012: Pattern Recognition in Bioinformatics pp 210–221Cite as

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Predicting V(D)J Recombination Using Conditional Random Fields

Predicting V(D)J Recombination Using Conditional Random Fields

  • Raunaq Malhotra23,
  • Shruthi Prabhakara23 &
  • Raj Acharya23 
  • Conference paper
  • 1658 Accesses

  • 1 Citations

Part of the Lecture Notes in Computer Science book series (LNBI,volume 7632)

Abstract

V(D)J gene segments undergo combinatorial recombination in the T-cells and B-cells to provide humans and other vertebrates with a large number of antibodies required for immunity. Each such recombination further undergoes mutations in their DNA sequences so that they can recognize diverse antigens. Predicting the combination of gene segments which formed a particular antibody is an essential task for studying disease propagation and analysis. We propose a model based on conditional random fields (CRFs) for predicting the boundary positions between V-D-J gene segments. We train the CRFs by generating synthetic gene recombinations using all of the alleles of the V, D and J gene segments. The alleles corresponding to a read can be determined by mapping the segmented reads to the DNA sequences of the gene segments using softwares like BLAST and usearch. We test our method on simulated dataset as well as real data of Stanford_S22 individual.

Keywords

  • Conditional Random Fields
  • VDJ recombination
  • Mapping of DNA sequences

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Author information

Authors and Affiliations

  1. Department of Computer Science Engineering, Pennsylvania State University, University Park, PA, 16801, USA

    Raunaq Malhotra, Shruthi Prabhakara & Raj Acharya

Authors
  1. Raunaq Malhotra
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  2. Shruthi Prabhakara
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  3. Raj Acharya
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Editor information

Editors and Affiliations

  1. Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, 108-8639, Minato-ku, Tokyo, Japan

    Tetsuo Shibuya

  2. Department of Mathematical Informatics, The University of Tokyo, 7-3-1 Hongo, 113-8654, Bunkyo-ku, Tokyo, Japan

    Hisashi Kashima

  3. Department of Comouter Science, Tokyo Institute of Technology, 2-12-1 Ookayamama, 152-8550, Meguro-ku, Tokyo, Japan

    Jun Sese

  4. Bioinformatics Project, National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, 567-0085, Suita, Osaka, Japan

    Shandar Ahmad

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© 2012 Springer-Verlag Berlin Heidelberg

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Malhotra, R., Prabhakara, S., Acharya, R. (2012). Predicting V(D)J Recombination Using Conditional Random Fields. In: Shibuya, T., Kashima, H., Sese, J., Ahmad, S. (eds) Pattern Recognition in Bioinformatics. PRIB 2012. Lecture Notes in Computer Science(), vol 7632. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-34123-6_19

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  • DOI: https://doi.org/10.1007/978-3-642-34123-6_19

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  • Print ISBN: 978-3-642-34122-9

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