Centro Singular de Investigación en Tecnoloxías Intelixentes (CiTIUS), Universidade de Santiago de Compostela, Rúa de Jenaro de la Fuente Domínguez, E15782, Santiago de Compostela, Spain.
Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), E15706, Santiago de Compostela, Spain.
BMC Bioinformatics. 2024 May 14;25(1):189. doi: 10.1186/s12859-024-05805-7.
The selection of primer pairs in sequencing-based research can greatly influence the results, highlighting the need for a tool capable of analysing their performance in-silico prior to the sequencing process. We therefore propose PrimerEvalPy, a Python-based package designed to test the performance of any primer or primer pair against any sequencing database. The package calculates a coverage metric and returns the amplicon sequences found, along with information such as their average start and end positions. It also allows the analysis of coverage for different taxonomic levels.
As a case study, PrimerEvalPy was used to test the most commonly used primers in the literature against two oral 16S rRNA gene databases containing bacteria and archaea. The results showed that the most commonly used primer pairs in the oral cavity did not match those with the highest coverage. The best performing primer pairs were found for the detection of oral bacteria and archaea.
This demonstrates the importance of a coverage analysis tool such as PrimerEvalPy to find the best primer pairs for specific niches. The software is available under the MIT licence at https://gitlab.citius.usc.es/lara.vazquez/PrimerEvalPy .
在基于测序的研究中，引物对的选择会极大地影响结果，这凸显了在测序前需要有一种能够在计算机上分析其性能的工具。因此，我们提出了 PrimerEvalPy，这是一个基于 Python 的软件包，旨在针对任何测序数据库测试任何引物或引物对的性能。该软件包计算了覆盖度指标，并返回了所发现的扩增子序列，以及它们的平均起始和结束位置等信息。它还允许对不同分类水平的覆盖度进行分析。
作为一个案例研究，我们使用 PrimerEvalPy 对文献中最常用的引物对进行了测试，这些引物对针对包含细菌和古菌的两个口腔 16S rRNA 基因数据库。结果表明，口腔中最常用的引物对与覆盖率最高的引物对不匹配。我们发现了用于检测口腔细菌和古菌的最佳引物对。
这表明需要使用像 PrimerEvalPy 这样的覆盖度分析工具来找到针对特定生态位的最佳引物对。该软件可在 MIT 许可证下在 https://gitlab.citius.usc.es/lara.vazquez/PrimerEvalPy 获得。
