How to archive an unannotated motif sequence via online method from NCBI

Preface
The sequence searching is a common work in molecular biology and diagnostics. Sometimes, it is ineluctability to obtain a rarely annotated sequence of a target strain of the species to meet the research requirements. This problem often came out from the international students around me. How to simply deal with the problem were their highly concerned. Therefore, the current push is mainly discussing about the online method to archive an unannotated sequence of a special strain.

Background

Get the Receptor Binding Domain (RBD) sequence of a special SARS-CoV-2 strain

        The RBD domain is a short immunogenic fragment from a virus that binds to a specific endogenous receptor sequence to gain entry into host cells. Specially, the RBD domain is a part of the spike protein. In Coronaviruses, the RBD domain in the spike protein works as a key part in the virus infection. Thus, the studies on RBD of the coronaviruses is meaningful in multiplex fields such as developing the vaccine against to the viruses like the one caused the COVID-19 pandemic.
        Here, let’s make a scenario simulation that if you isolate and sequence a SARS-CoV-2 strain from a COVID-19 patient and you want to check if there are some variations across the RBD domain of your isolated strain compared with the reference genome. How could you perform the analysis? I am sure most of you guys wants alignment your sequenced genome with the reference genome and extract the RBD sequence based on the reference annotation information. However, there is no RBD related information in the website of the SARS-CoV-2 reference genome (NC_045512.2).

Method

        The protein database in the NCBI has the information we need. Click the linkage YP_009724390.1 showed in the last picture, later a new window will be shown as follows

        The information about RBD sequence is shown in this page

        The RBD will be shown and downloaded after you click the linkage “Region”.

        With the execution above, any motif if are not annotated in the main page of the whole genome of a special species could be archived correctly.

Additional

        An other website named PDB database (https://www.rcsb.org/) also stored the information we want. Additionally, the PDB database is not only storing the sequence information we want, but also the three-dimensional structure. With these information, more meaningful works can be performed. The part of the PDB database will be introduced later.