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How to blastp

Hello everyone,

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!

genome blast
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updated by Ram Ram • written by frenchmytoast112 • frenchmytoast112

1 answer

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 nr as -db. To perform search on the NCBI server you can select the flag -remote.

See blast option here.

• 0 views • link
updated by Ram Ram • written by dago dago

What is the difference between the genomes in my .faa and the nr database? Shouldnt first download the genome from the nr database? And my sequence is from a separate genome and has nothing to do with the ones I am trying to blast.

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written by frenchmytoast112 • frenchmytoast112

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