Maybe it is a very silly question to ask. I am a newcomer in Bioinformatics.
I want to collect the nucleotide sequence of the complete genome of a certain virus. But, for my study, I need the sequence of all strains available in NCBI. Firstly, I tried a simple straightforward method, that is I put the name of the virus in the NCBI search box and select nucleotide as a database. But, the returned result seemed to be very messy, as there were many sequences with partial genome or even with a specific gene. In that case, I had to check all the results manually and then collect the sequences. But there were thousands of results for my search text.
So, I think there must be a useful technical way to download the nucleotide sequence of all strains of a certain virus.
Would you please suggest me any solution?
Once way to use NCBI Taxonomy. For example putting "Dengue virus" here https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi and clicking assemblies radio button "assemblies" gives 6 .
You may want to try the viral genome section of the NCBI website.
You can also go here. Limit to genome you are interested in.