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Modeling for Evaluation of Significant Features in siRNA Design

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Contemporary Computing (IC3 2010)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 94))

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Abstract

RNAi is the most conserved phenomenon occurring in eukaryotes, where it controls the developmental process through gene regulation. Recently, exogenously generated siRNA mediated RNAi has drawn greater significance in functional genomics and therapeutic applications like cancer, HIV and neurodegenerative diseases specially in mammalian system. Computational designing of efficient sequence specific siRNAs against the gene of interest deploy many guidelines, which are based upon sequence to thermodynamic features as a pivotal determinants of effective siRNA sequences, but identification of optimal features needed for efficient designing are yet to be deciphered in the assurance of better efficacy. Till date many computational tools are available, but no tool provide the accurate gene specific siRNA sequences with absolute efficacy therefore study of suitable features of siRNA design is very smoldering issue to be solved in the present scenario. In the present work, we have applied ant colony optimization technique to indentify the features of siRNA up to considerable amount of accuracy and further the results are modeled using four independent models such as linear regression, ANCOVA, libSVM and liblinear with the conclusion that linear features are preferentially superior then thermodynamic features while both group of features are important in the efficacy prediction of siRNA. The results are highly coherence with prior investigations and highlight the importance of sequential features in effective siRNA design.

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Author information

Authors and Affiliations

  1. Department of Biotechnology, Jaypee Institute of Informtion Technology University, Noida, India

    Chakresh Kumar Jain

  2. Department of Computer Science and Engineering, Indian Institute of Technology, Delhi, India

    Yamuna Prasad

Authors
  1. Chakresh Kumar Jain
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  2. Yamuna Prasad
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Editor information

Editors and Affiliations

  1. Dept. of Computer Sciences, University of Florida, 32611, Gainesville, FL, USA

    Sanjay Ranka

  2. University of Florida, Gainesville, Fl, USA

    Arunava Banerjee

  3. Department of Computer Science and Engineering, Indian Institute of Technology, 110016, New Delhi, INDIA

    Kanad Kishore Biswas

  4. Computer Science, College of Engineering and Science, Louisiana Tech University, LA 71272, Ruston, USA

    Sumeet Dua

  5. University of Florida, Gainesville, FL, USA

    Prabhat Mishra

  6. Department of Computer Science & Engineering, Indian Institute of Technology, 208016, Kanpur, India

    Rajat Moona

  7. National Tsing Hua University, Hsin-Chu, Taiwan, R.O.C.

    Sheung-Hung Poon

  8. Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong

    Cho-Li Wang

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Jain, C.K., Prasad, Y. (2010). Modeling for Evaluation of Significant Features in siRNA Design. In: Ranka, S., et al. Contemporary Computing. IC3 2010. Communications in Computer and Information Science, vol 94. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-14834-7_52

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  • DOI: https://doi.org/10.1007/978-3-642-14834-7_52

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-14833-0

  • Online ISBN: 978-3-642-14834-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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