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bioinformaticsblastprotein-database

BLAST: blastpgp not producing an output file, unsure if using database flag correctly

Question 1:

I'm running the following:

blast-2.2.26/bin/blastpgp -i protein.fasta -j 5 -o file -d nr

where protein.fasta is a fasta file containing a single protein sequence. This produces no output and the -o file is empty.

Question 2:

I was able to successfully use:

blast-2.2.26/bin/formatdb -i family_of_proteins.fas -o T -s T

to create database files. However, this produced multiple files, .phr, .pin, .psd, .psi, .psq. Which one of these should I pass with the -d flag to use my own database?

Thank you!

Solution

  • For question 2:

    You should pass the base name with the -d flag, so in you example, it would be "-d family_of_proteins.fas"