How to check the indexed database with makeblastdb

[angeloulivieri]

Hi all,
as I wrote in the title, I would like to know if there's a way to check the consistency of an indexed database once I used makeblastdb.

thanks you all

Angelo

[mastal]

How to check the indexed database with makeblastdb

Have a look at the blast manual.

http://www.ncbi.nlm.nih.gov/books/NBK1763/

You can use 'blastdbcmd -info' (see the syntax in the manual) to check if your database was created properly, and you can use other options with the blastdbcmd command to check that blast knows where to look for your database.

[angeloulivieri]

I seen that actually, using this command, I can get the informations about the database.

blastdbcmd -db hs_chr -info

No other description is written on the manual and in the blastdbcm -help I found that this options is the only one that can give me an useful information about.

What if the indexed database is not consistent..? No informations will be displayed?
Since I'm working with PERL I wanted to add a control about an automatically indexed db, this is the reason why I'm searching for this kind of command.

[angeloulivieri]

[solved]

I think that I can do this.
I seen that blastdbcmd gives a result when the indexed file is well done. Otherwise it will give an error like the normal BLAST programs

BLAST Database error: No alias or index file found for nucleotide database [name.fasta] in search path [/home/test::]

and it will not create the output file when used the -out parameter.

So simply I can check if the output file exists or is empty.

bye!