Question: How to blastp
gravatar for frenchmytoast112
4.2 years ago by
frenchmytoast11210 wrote:

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!


blast genome • 1.4k views
ADD COMMENTlink modified 4.2 years ago by dago2.6k • written 4.2 years ago by frenchmytoast11210

You could write a script to send your queries to the NCBI server. BioPerl has Bio::Tools::Run::RemoteBlast for this or you can roll your own using the NCBI Blast API. Just be careful not to hammer their server or you may get banned from it.

ADD REPLYlink written 4.2 years ago by Jean-Karim Heriche22k
gravatar for dago
4.2 years ago by
dago2.6k wrote:

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.

ADD COMMENTlink modified 3 months ago by RamRS26k • written 4.2 years ago by dago2.6k

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.

ADD REPLYlink written 4.2 years ago by frenchmytoast11210
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