Accessing blast nt database

Question

[langziv]

Hello.

I wish to customize the blast database the installed on my server. The database path includes binary files which can't be read. How can one read the content of the database?

Answer 1

[GenoMax]

I wish to customize the blast database the installed on my server

You can't do anything to the pre-made binary database files. If you want to customize the nt database you could download the fasta files for nt from this folder and then edit out anything you don't want and then re-make blast indexes from the edited file.

That said, it may be simpler to use some combination of -taxids, -taxidlist and -entrez_query options available in blast+ programs to limit your searches with the existing database.

Answer 2

[dariober]

I think this https://bioinformatics.stackexchange.com/questions/815/how-to-extract-fasta-from-a-blastdb should answer your question?

[langziv]

I tried that and got an error message that says that the database name is wrong. The command I entered was

blastdbcmd -entry all -db nt.gz -out -reference.fasta

I also tried nt and taxdb instead of nt.gz.

[GenoMax]

nt.gz is not the index basename. It should be just nt. Once you get the command right it will dump out contents of entire nt database into a file in fasta format. You could get that file directly from the link I provided above.