I downloaded and extract blast nt.24 database, but when I run :
blastn -task blastn-short -query consulta.fa -db nt.24 -out misalida.txt
it says: mdb_env_open: No such file or directory
and if a try with nt instead of nt.24 it says:
BLAST Database error: Could not find volume or alias file (nt.00) referenced in alias file (/root/my-documents/blastdb/nt/nt So my question is :
Do I have to download all nt.xx files?
And : Will it show the organisms in the output result?
In general, yes, you do need to download and extract all (nt.00 - nt.46 as of now) of the nt portions in order to do a comprehensive BLAST against all of nt. The database has been split up for convenience (to make smaller individual files), so all are necessary to be comprehensive.
Once you download all the pieces, you’ll want to use nt as the database parameter to blastn.
blastn -task blastn-short -query consulta.fa -db nt -out misalida.txt
As for the second question - this depends on how you run the BLAST. Each accession is associated with a taxid, which will map to its taxonomy. This can be mapped back to the organism, but you may need to do some interpretation in order to convert the BLAST hits to the proper organism - this depends highly on what kind of sequences you are aligning.
Thanks, I downloaded nt.00 (by http firefox because wget via ftp always returned a corrupted file when decompressing it) and it works fine locally. The command is:
blastn -task blastn-short -query consulta.fa -db nt.00 -out misalida.txt
I also added a first line >Seq1 to the query file consulta.fa (if not didn't work):>Seq1 GTGCC...
And the results in misalida.txt first print the taxid with the organism name and chromosome. At the bottom it printed the positions details. What I'm doing is a genome editor, so when you enter some nucleotids(like 14 to 20 or more) it will search with blastn possible next nucleotids paths from many organisms with blastdbcmd.
