Siegmund Karsten H, Steiner Ulrich E, Richert Clemens
Institute for Organic Chemistry, University of Karlsruhe (TH), D-76128 Karlsruhe, Germany.
J Chem Inf Comput Sci. 2003 Nov-Dec;43(6):2153-62. doi: 10.1021/ci034049a.
Presented here is the program ChipCheck that allows the computation of total hybridization equilibria for hybridization experiments involving small oligonucleotide arrays. The calculation requires the free energies of binding for all pairs of probes and targets as well as total strand concentrations and probe molecule numbers. ChipCheck has been tested computationally on microarrays with up to 100 spots and 42 target strands (4200 binding equilibria). It arrives at solutions through iterations employing the multidimensional Newton method. While currently running in simulation mode only, an extension of the approach to the exhaustive analysis of chip results is being outlined and may be implemented in the future. The output displays the extent of correct and cross hybridization both graphically and numerically. In principle, calculating total hybridization equilibria allows for eliminating noise from DNA chip results and thus an improvement in sensitivity and accuracy.
这里展示的是ChipCheck程序，它可以计算涉及小寡核苷酸阵列的杂交实验的总杂交平衡。该计算需要所有探针与靶标对的结合自由能，以及总链浓度和探针分子数。ChipCheck已在多达100个点和42条靶标链（4200个结合平衡）的微阵列上进行了计算测试。它通过使用多维牛顿法的迭代得出解决方案。虽然目前仅在模拟模式下运行，但正在概述将该方法扩展到芯片结果的详尽分析，并且可能在未来实施。输出以图形和数字方式显示正确杂交和交叉杂交的程度。原则上，计算总杂交平衡可以消除DNA芯片结果中的噪声，从而提高灵敏度和准确性。
