protein blast database in fasta format

Question

[seta]

Hi all,

I have made a blast database as a protein type, which include 6 type of file with the prefixes of .phr, .pin, .pog, .psd, .psi, .psg. Now, I want to send this database as a fasta format for my friend to run blast. As you know, these file are as binary format, could you please let me know how I can send them as a fasta format?

Thanks

Answer 1

[5heikki]

I'm pretty sure this is in the manual..

blastdbcmd -entry all -db ?? > out.fasta

In case there's redundancy also note the -ctrl_a option. Depending what you want, you might also want to first extract all ids and then -batch_entry and -target_only

[seta]

Thanks dear friend