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© Oxford University Press

SUBTRACT: a computer program for modeling the process of subtractive hybridization

Olga D. Ermolaeva 2 and Mark C. Wagner 1

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10 Miklukho-Maklaya, Moscow, 117871, Russia
1Human Genome Center, Lawrence Livermore National Laboratory 7000 East Avenue L-452, Livermore, CA 94550, USA

2To whom correspondence should be addressed. Email: ermolaevaola{at}glas.apc.org

We report on a new software tool, SUBTRACT, which allows the analysis of the possible strategies for an experiment based on a mathematical model of subtractive hybridization. The program helps the experimenter choose the optimal strategy and conditions for performing the reaction. The program allows the modeling of cDNA and genomic subtraction for different types of target DNA. SUBTRACT offers a friendly interface for the investigation of the dynamics of the process of subtractive hybridization, and for modifying different parameters and initial conditions. SUBTRACT allows the user to plot the values of interesting quantities as a function of the reaction time. The program runs under the Unix operating system on Sun-compatible computers.


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