How To Set Own Protein Fasta File As Database In Ncbi-Blast-2.2.28

Question

[Naren]

I have installed NCBI-Blast-2.2.28 on win-7.
Also set the path variable to bin directory. I want my protein fasta file to be used as database. against protein query with few sequences. (all vs all).

Upon following commands:

 blastdbcmd -db my_db.fasta  -outfmt "%f" -out query.fasta.txt

 blastp -query query.fasta -db my_db.fasta -out output.txt

Error: No alias or index file found for protein database

(files are present in folder specified).

Where I might have gone wrong?

Answer 1

[Michael]

You should read the fine Blast+ documentation. you need to run makeblastdb to format a database first. You can't use blastdbcmd on a fasta file. You can use blastp with -subject my.fasta instead of -db.