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1 Foundations of Computing and Decision Sciences

1 2007

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

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Błażewicz J. , Dziurdza B. , Markiewicz W. T. , Oguz C.

tom Vol. 32, No. 3

185-197

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.