I want to download a specific gene from multiple genomes. In this case, I want to download just the S gene from different coronaviruses. I would like to be able to provide taxonomic IDs and the gene name, and then download all distinct, verified sequences of that gene.
I do know how to download whole genomes, but I do not want the whole genomes because that would unnecessarily complicate downstream analysis.
I am not very proficient with the tools of bioinformatics, so I will appreciate any guidance (and patience).
There are some lackings in bioinformatics if I am not wrong.
First, identify your gene and go for expression analysis. Try Ensemble, it allows you to align and to make genes out.
Shamsunnahar Mukta Thank you for your answer. Unfortunately Ensemble does not include viral genes. Secondly, I don't want the assembly version of each gene because I would like to examine selective pressure on each codon, so I need all sequences of that gene that have been submitted.
Then try expression analysis... It will give you the map of the presence of the gene with its expression... Please let me know if you find any other solution.
I prefer JGI for single gene searches. You can either select the genomes for your search, or search all genomes.
as Yasmin Sabino said, you need only to go to NCBI, check for your gene and make a blastP for the corresponding protein or blastX directly from the gene. I would run it searching for orthologous proteins which means a high coverage and identity (>50% and >80%).
Best.
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