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On the computational complexity of designing DNA randomizations in a combinatorial protein experiment

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Warianty tytułu
Języki publikacji
EN
Abstrakty
EN
In combinatorial protein experiments based on phage display and similar methods, protein libraries are constructed by expressing a partially randomized DNA (gene) libraries. Since the distribution of proteins in the output library depends on nucleotides frequencies in DNA library one has to adjust them carefully taking into account diversity-completeness trade-off and results from possible previous cycles of experiments (i.e. knowledge about sequences that have been already obtained and tested). The approach considered in this paper allows to maximize the number of new amino acid sequences physically generated in each cycle of the experiment. The mathematical model of the described approach is presented and its computational complexity is analyzed.
Rocznik
Strony
185--197
Opis fizyczny
Bibliogr. 10 poz.
Twórcy
autor
autor
  • Institute of Computing Science, Poznań University of Technology, Piotrowo 3A, 60-965 Poznań, Poland Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
Bibliografia
  • [1] Steipe, B. (1999) Evolutionary Approaches to Protein Engineering. Current Topics in Microbiology and Immunology: Combinatorial Chemistry in Biology. 243. 56-81
  • [2] Smith, G.P., Petrenko V.A. (1997) Phage Display. Chem. Rev-. 97, 391-410
  • [3] Patrick W,M., Firth A.E., Blackburn J.M. (2003) User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries. Protein Eng. 16, 451-457
  • [4] Wang, W.. Saven, J. G. (2002). Wang, W., Saven. J. G. (2002). Designing gene libraries from protein profiles for combinatorial protein experimenl.fi. Nucleic Acids Res.. 30, e!20
  • [5] Brian Ward and Thomas Juehne (1998) Combinatorial library diversity: probability assessment of library populations Nucleic. Acids Research, 26, 879-886
  • [6] Blażewicz J,, Dziurdza B., Markiewicz W. T., Oguz C.(2006) The parallel genetic algorithm for designing DNA randomizations in a combinatorial protein experiment LNCS, 3911, 1097-1105
  • [7] Dziurdua, B., Blażewicz J., Markiewicz W. T. (2003) Artificial evolution. Algorithms for searching for amino acid sequences. RECOMB 2003. Currents in Computational Molecular Biology, 151-152
  • [8] Blażewicz J., Dziurdza, B., Markiewicz W. T. (2003) Artificial evolution. An algorithm for an exploration of the amino acid sequences space. Foundations of Computing and Decision Sciences. 28. 195-209
  • [9] Waterman. M. S.. Introduction to Computational Biology. Maps, Sequences and Genomes, Chapman & Hall, 1995
  • [10] Garey, M, R... Johnson D. S-, Computers and Intractib-Uity, W. II. Freeman and Company, 1979
Typ dokumentu
Bibliografia
Identyfikator YADDA
bwmeta1.element.baztech-article-BPP1-0079-0066
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