Kalendar Ruslan, Khassenov Bekbolat, Ramankulov Yerlan, Samuilova Olga, Ivanov Konstantin I
PrimerDigital Ltd, FIN-00710 Helsinki, Finland.
RSE "National Center for Biotechnology" under the Science Committee, Ministry of Education and Science of the Republic of Kazakhstan, Astana, Kazakhstan.
Genomics. 2017 Jul;109(3-4):312-319. doi: 10.1016/j.ygeno.2017.05.005. Epub 2017 May 12.
Polymerase chain reaction (PCR) is one of the most important laboratory techniques used in molecular biology, genetics and molecular diagnostics. The success of a PCR-based method largely depends on the correct nucleic acid sequence analysis in silico prior to a wet-bench experiment. Here, we report the development of an online Java-based software for virtual PCR on linear or circular DNA templates and multiple primer or probe search from large or small databases. Primer or probe sensitivity and specificity are predicted by searching a database to find sequences with an optimal number of mismatches, similarity and stability. The software determines primer location, orientation, efficiency of binding and calculates primer melting temperatures for standard and degenerate oligonucleotides. The software is suitable for batch file processing, which is essential for automation when working with large amounts of data. The online Java software is available for download at http://primerdigital.com/tools/pcr.html. Accession numbers for the sequences resulting from this study: EU140956 EU177767 EU867815 EU882730 FJ975775-FJ975780 HM481419 HM481420 KC686837-KC686839 KM262797.
聚合酶链反应（PCR）是分子生物学、遗传学和分子诊断学中最重要的实验室技术之一。基于PCR方法的成功很大程度上取决于在湿实验台实验之前在计算机上进行的正确核酸序列分析。在此，我们报告了一种基于Java的在线软件的开发，该软件用于对线性或环状DNA模板进行虚拟PCR，并从大型或小型数据库中进行多个引物或探针搜索。通过搜索数据库以找到具有最佳错配数、相似性和稳定性的序列来预测引物或探针的敏感性和特异性。该软件确定引物位置、方向、结合效率，并计算标准和简并寡核苷酸的引物解链温度。该软件适用于批处理文件，这对于处理大量数据时的自动化至关重要。该在线Java软件可从http://primerdigital.com/tools/pcr.html下载。本研究产生的序列的登录号：EU140956、EU177767、EU867815、EU882730、FJ975775 - FJ975780、HM481419、HM481420、KC686837 - KC686839、KM262797。
