JOURNAL OF LIGHT INDUSTRY

CN 41-1437/TS  ISSN 2096-1553

Volume 31 Issue 4
July 2016
Article Contents
FANG Gang. Protein expression vector optimization based on statistical language model and dynamic programming[J]. Journal of Light Industry, 2016, 31(4): 88-94. doi: 10.3969/j.issn.2096-1553.2016.4.013
Citation: FANG Gang. Protein expression vector optimization based on statistical language model and dynamic programming[J]. Journal of Light Industry, 2016, 31(4): 88-94. doi: 10.3969/j.issn.2096-1553.2016.4.013 shu

Protein expression vector optimization based on statistical language model and dynamic programming

  • Received Date: 2016-04-13
    Available Online: 2016-07-15
  • In order to solve the problem of time consuming and error pronein selecting optimal "brick" to assemble functional protein expression vector,based on statistical language model (SLM), a dynamic programming algorithm of protein expression vector was carried out. By collecting the statistical parameters of BioBrick standard parts and transforming the assembling process into SLM, a dynamic programming algorithm could be performed to choose suitable parts to compose the final genetic construction. The result showed this method had high accuracy,redundant operations could be reduced and the time and cost required for conducting biological experiment could be minimized. The method could be not only used to optimize a design in a synthetic biological robotic platform, but also independently used to automate the DNA assembly process in synthetic biology. It could also be iterated and then give out different optimized results for consideration.
  • 加载中
    1. [1]

      GOLER J A,BRAMLETT B W,PECCOUD J.Genetic design:rising above the sequence[J].Trends Biotechnol,2008,26:538.

    2. [2]

      GRASLUND S,NORDLUND P,WEIGELT J,et al.Protein production and purification[J].Nat Methods,2008(5):135.

    3. [3]

      CZAR M J,CAI Y,PECCOUD J.Writing DNA with GenoCAD[J].Nucleic Acids Res,2009,37:W40.

    4. [4]

      CAI Y,WILSON M L,PECCOUD J.GenoCAD for iGEM:a grammatical approach to the design of standard-compliant constructs[J].Nucleic Acids Res,2010,38:2637.

    5. [5]

      ISAACS F J,DWYER D J,DING C,et al.Engineered riboregulators enable posttranscriptional control of gene expression[J].Nat Biotechnol,2004,22:841.

    6. [6]

      GARDNER T S,CANTOR C R,COLLINS J J.Construction of a genetic toggle switch in Escherichia coli[J].Nature,2000,403:339.

    7. [7]

      ADAMES N R,WILSON M L,FANG G,et al.GenoLIB:a database of biological parts derived from a library of common plasmid features[J].Nucleic Acids Res,2015,43:4823.

    8. [8]

      ARKIN A.Setting the standard in synthetic biology[J].Nat Biotechnol,2008,26:771.

    9. [9]

      CANTON B,LABNO A,ENDY D.Refinementand standardization of synthetic biological parts and devices[J].Nat Biotechnol,2008,26:787.

    10. [10]

      DENSMORE D,HSIAU T H C,BATTEN C,et al.Algorithms for automated DNA assembly[J].Nucleic Acids Res,2010,38:2607.

    11. [11]

      COLL A,WILSON M L,GRUDEN K,et al.Rule-based design of plant expression vectors using GenoCAD[J].PLoS ONE,2015,10(7):e0132502.

    12. [12]

      JELINEK F.Statistical Methods for Speech Recognition (Language,Speech,and Communication)[M].Cambridge:MIT Press,1998.

    13. [13]

      CAI Y,HARTNETT B,GUSTAFSSON C,et al.A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts[J].Bioinformatics,2007,23:2760.

    14. [14]

      CHEN S F,GOODMAN G.An empirical study of smoothing techniques for language modeling[J].Computer Speech and Language,1999(13):359.

    15. [15]

      VITERBI A J.A personal history of the viterbi algorithm[J].IEEE Signal Processing Magazine,2006,23:120.

    16. [16]

      HUANG F L,YU M S,HWANG C Y.An empirical study of good-turing smoothing for language models on different size corpora of Chinese[J].Journal of Computer and Communications,2013(1):14.

    17. [17]

      KATZ S M.Estimation of probabilities from sparse data for the language model component of a speech recogniser[J].IEEE Transactions on Acoustics (Speech and Signal Processing),1987,35:400.

Article Metrics

Article views(1586) PDF downloads(62) Cited by()

Ralated
    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return