Interdisciplinary Neuroscience Program, Bilkent University, Ankara, Turkey.
Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.
Genomics. 2021 Sep;113(5):3174-3184. doi: 10.1016/j.ygeno.2021.07.020. Epub 2021 Jul 20.
As mutations in SARS-CoV-2 virus accumulate rapidly, novel primers that amplify this virus sensitively and specifically are in demand. We have developed a webserver named CoVrimer by which users can search for and align existing or newly designed conserved/degenerate primer pair sequences against the viral genome and assess the mutation load of both primers and amplicons. CoVrimer uses mutation data obtained from an online platform established by NGDC-CNCB (12 May 2021) to identify genomic regions, either conserved or with low levels of mutations, from which potential primer pairs are designed and provided to the user for filtering based on generalized and SARS-CoV-2 specific parameters. Alignments of primers and probes can be visualized with respect to the reference genome, indicating variant details and the level of conservation. Consequently, CoVrimer is likely to help researchers with the challenges posed by viral evolution and is freely available at http://konulabapps.bilkent.edu.tr:3838/CoVrimer/.
随着 SARS-CoV-2 病毒的突变迅速积累，人们迫切需要能够灵敏且特异性地扩增这种病毒的新型引物。我们开发了一个名为 CoVrimer 的网络服务器，用户可以通过该服务器搜索并将现有的或新设计的保守/简并引物对序列与病毒基因组进行比对，并评估引物和扩增子的突变负荷。CoVrimer 使用来自 NGDC-CNCB 建立的在线平台（2021 年 5 月 12 日）获得的突变数据，从其中鉴定出保守或突变水平较低的基因组区域，然后设计潜在的引物对，并根据通用和 SARS-CoV-2 特异性参数提供给用户进行筛选。可以根据参考基因组对引物和探针进行比对，显示变异细节和保守程度。因此，CoVrimer 可能有助于研究人员应对病毒进化带来的挑战，可在 http://konulabapps.bilkent.edu.tr:3838/CoVrimer/ 免费获得。
