The aim of this paper is to improve the best known solution of an important problem, the DNA Word Design problem, which has its roots in Bioinformatics and Coding Theory. The problem is to design DNA codes that satisfy some combinatorial constraints. The constraints considered are: minimum Hamming distance, fixed GC content and the reverse complement Hamming distance. The problem is modeled as a maximum independent set problem. Existing complex approaches for the maximum independent set problem, suitable for large graphs, were tested. In order to tackle large instances, libraries for external memory computations and sampling techniques were investigated. Eventually, we succeed in finding good lower bounds for the instances that were analyzed.

中文翻译：

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DNA 词设计问题的基于图的方法

本文的目的是改进一个重要问题的最佳解决方案，即 DNA 字设计问题，该问题源于生物信息学和编码理论。问题是设计满足某些组合约束的 DNA 代码。考虑的约束是：最小汉明距离、固定的 GC 内容和反向补码汉明距离。该问题被建模为最大独立集问题。对适用于大图的最大独立集问题的现有复杂方法进行了测试。为了处理大型实例，研究了用于外部存储器计算和采样技术的库。最终，我们成功地为所分析的实例找到了良好的下界。