Milewski Marek C, Kamel Karol, Kurzynska-Kokorniak Anna, Chmielewski Marcin K, Figlerowicz Marek
1 Institute of Bioorganic Chemistry PAS , Poznan, Poland .
2 Institute of Computing Science, Poznan University of Technology , Poznan, Poland .
J Comput Biol. 2017 Oct;24(10):1014-1028. doi: 10.1089/cmb.2016.0154. Epub 2017 Mar 15.
Experimental methods based on DNA and RNA hybridization, such as multiplex polymerase chain reaction, multiplex ligation-dependent probe amplification, or microarray analysis, require the use of mixtures of multiple oligonucleotides (primers or probes) in a single test tube. To provide an optimal reaction environment, minimal self- and cross-hybridization must be achieved among these oligonucleotides. To address this problem, we developed EvOligo, which is a software package that provides the means to design and group DNA and RNA molecules with defined lengths. EvOligo combines two modules. The first module performs oligonucleotide design, and the second module performs oligonucleotide grouping. The software applies a nearest-neighbor model of nucleic acid interactions coupled with a parallel evolutionary algorithm to construct individual oligonucleotides, and to group the molecules that are characterized by the weakest possible cross-interactions. To provide optimal solutions, the evolutionary algorithm sorts oligonucleotides into sets, preserves preselected parts of the oligonucleotides, and shapes their remaining parts. In addition, the oligonucleotide sets can be designed and grouped based on their melting temperatures. For the user's convenience, EvOligo is provided with a user-friendly graphical interface. EvOligo was used to design individual oligonucleotides, oligonucleotide pairs, and groups of oligonucleotide pairs that are characterized by the following parameters: (1) weaker cross-interactions between the non-complementary oligonucleotides and (2) more uniform ranges of the oligonucleotide pair melting temperatures than other available software products. In addition, in contrast to other grouping algorithms, EvOligo offers time-efficient sorting of paired and unpaired oligonucleotides based on various parameters defined by the user.
基于DNA和RNA杂交的实验方法，如多重聚合酶链反应、多重连接依赖探针扩增或微阵列分析，需要在单个试管中使用多种寡核苷酸（引物或探针）的混合物。为了提供最佳反应环境，必须使这些寡核苷酸之间的自杂交和交叉杂交降至最低。为了解决这个问题，我们开发了EvOligo，这是一个软件包，提供了设计和分组具有特定长度的DNA和RNA分子的方法。EvOligo结合了两个模块。第一个模块进行寡核苷酸设计，第二个模块进行寡核苷酸分组。该软件应用核酸相互作用的最近邻模型并结合并行进化算法来构建单个寡核苷酸，并对具有尽可能弱的交叉相互作用特征的分子进行分组。为了提供最佳解决方案，进化算法将寡核苷酸分类为集合，保留寡核苷酸的预选部分，并塑造其其余部分。此外，寡核苷酸集合可以根据其解链温度进行设计和分组。为方便用户，EvOligo提供了用户友好的图形界面。EvOligo用于设计具有以下参数特征的单个寡核苷酸、寡核苷酸对和寡核苷酸对组：（1）非互补寡核苷酸之间的交叉相互作用较弱；（2）与其他现有软件产品相比，寡核苷酸对解链温度范围更均匀。此外，与其他分组算法不同，EvOligo基于用户定义的各种参数，提供了对配对和未配对寡核苷酸的高效排序。
