Mokhtar Morad M, Alsamman Alsamman M, El Allali Achraf
Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Benguerir, Morocco.
Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza, Egypt.
Front Plant Sci. 2023 Dec 14;14:1219055. doi: 10.3389/fpls.2023.1219055. eCollection 2023.
Next-generation sequencing technologies have opened new avenues for using genomic data to study and develop molecular markers and improve genetic resources. Simple Sequence Repeats (SSRs) as genetic markers are increasingly used in molecular diversity and molecular breeding programs that require bioinformatics pipelines to analyze the large amounts of data. Therefore, there is an ongoing need for online tools that provide computational resources with minimal effort and maximum efficiency, including automated development of SSR markers. These tools should be flexible, customizable, and able to handle the ever-increasing amount of genomic data. Here we introduce MegaSSR (https://bioinformatics.um6p.ma/MegaSSR), a web server and a standalone pipeline that enables the design of SSR markers in any target genome. MegaSSR allows users to design targeted PCR-based primers for their selected SSR repeats and includes multiple tools that initiate computational pipelines for SSR mining, classification, comparisons, PCR primer design, PCR validation, and statistical visualization. MegaSSR results can be accessed, searched, downloaded, and visualized with user-friendly web-based tools. These tools provide graphs and tables showing various aspects of SSR markers and corresponding PCR primers. MegaSSR will accelerate ongoing research in plant species and assist breeding programs in their efforts to improve current genomic resources.
新一代测序技术为利用基因组数据研究和开发分子标记以及改善遗传资源开辟了新途径。简单序列重复（SSRs）作为遗传标记越来越多地用于分子多样性和分子育种计划中，这些计划需要生物信息学管道来分析大量数据。因此，持续需要在线工具，这些工具能以最小的工作量和最高的效率提供计算资源，包括SSR标记的自动化开发。这些工具应灵活、可定制，并且能够处理不断增加的基因组数据量。在此，我们介绍MegaSSR（https://bioinformatics.um6p.ma/MegaSSR），这是一个网络服务器和一个独立的管道，可在任何目标基因组中设计SSR标记。MegaSSR允许用户为其选定的SSR重复序列设计基于PCR的靶向引物，并包括多个工具，这些工具启动用于SSR挖掘、分类、比较、PCR引物设计、PCR验证和统计可视化的计算管道。可以使用用户友好的基于网络的工具访问、搜索、下载和可视化MegaSSR结果。这些工具提供显示SSR标记和相应PCR引物各个方面的图表。MegaSSR将加速当前植物物种的研究，并协助育种计划努力改善当前的基因组资源。
