Identify conserved regions in SARS-COV2 virus based on Multiple sequence alignment for primer design

Question

[Mohamed Elsherbieny]

As a part of my project, i am supposed to download sequences from (GISAID) that are representative of the 3 waves inside Africa and perform multiple sequence alignment, based on which i should find the conserved region to use as a target for primer design. I am wondering if there is a certain tool or script that would do so? and what parameters can i set for choosing the most accurate conserved region in terms of length and position, gaps etc

Answer 1

[Mensur Dlakic]

There are lots of resources for this, and you will find many more by doing a deeper Google search:

• https://www.biorxiv.org/content/10.1101/2020.03.10.985150v1
• https://academic.oup.com/ve/article/7/1/veab006/6128533
• https://www.thno.org/v10p7150.htm
• https://www.nature.com/articles/s41598-020-80363-5
• https://www.nature.com/articles/s12276-020-0452-7

[Mohamed Elsherbieny]

I gave them a quick read, couldn't find any mention of tools or scripts used to identify and extract conserved region from multiple sequence alignment file