I am looking to perform blastp with a few sequences on a few hundred genomes using the nr database.
My progress thus far involves:
1) I know there is the NCBI website for blastp. However, I am not sure how I can make the input for many genomes. I know the taxid, gi and acc for my genomes but I would not rather type the taxid for each of my genomes into the input bar (for the nr database).
2) I found out I can use the blast+ suite on my Ubuntu. Again, I am not sure how to use it. I found some tutorials to create my own databases, but since I have low computational power on my laptop I would rather like to send my files to the NCBI server. So how can I do properly?
Thanks a lot in advance!
If you want to perform a blastp search for the protein encoded in you genome, you can use the .faa of your genomes as
-query in blasp and select
-db. To perform search on the NCBI server you can select the flag
See blast option here.