Naive question about blast db

Question

[anasofiamoreira94]

hello, im sorry for the naive question, i hadn't used blast remotely, until this year. So, i want to run blast against all nt databses. i don't understand how to call the database. should i call the directori were i have the nts? Thanks

[GenoMax]

i hadn't used blast remotely, until this year

On the off-chance that you actually want to use blast+ installed locally but with databases located at NCBI, you would need to add -db blastb -remote to your command line.

Answer 1

[h.mon]

The path to the directory + "nt". Suppose you files are located in the folder /path/blastdb, such as

ls /path/blastdb/

Returns:

/path/blastdb/nt.00.nhd
/path/blastdb/nt.00.nhi
/path/blastdb/nt.00.nhr
/path/blastdb/nt.00.nin
...
/path/blastdb/nt.nal

So you have to use -db /path/blastdb/nt.

[anasofiamoreira94]

Thanks for the reply

[anasofiamoreira94]

I'm so sorry to boder you, i've already download the nt databases and then i tryied to do the blast:

blastn -query sample.fasta -db /path/blastdb/nt  -task megablast -outfmt 6 –max_target_seqs 10 > Resultado.txt

however, i have this error: No alias or index file found for nucleotide database

Thanks very much

[h.mon]

What ls /path/blastdb/nt* and ls /path/blastdb/nt.nal show?

[anasofiamoreira94]

When i do ls /path/blastdb/nt it outputs the lists: (example)

C:\ncbi-blast-2.8.0+\bin\all_nt\nt.60.nhd
C:\ncbi-blast-2.8.0+\bin\all_nt\nt.60.nhi
C:\ncbi-blast-2.8.0+\bin\all_nt\nt.60.nhr
C:\ncbi-blast-2.8.0+\bin\all_nt\nt.60.nin
C:\ncbi-blast-2.8.0+\bin\all_nt\nt.60.nnd
C:\ncbi-blast-2.8.0+\bin\all_nt\nt.60.nni
C:\ncbi-blast-2.8.0+\bin\all_nt\nt.60.nog
C:\ncbi-blast-2.8.0+\bin\all_nt\nt.60.nsd
C:\ncbi-blast-2.8.0+\bin\all_nt\nt.60.nsi
C:\ncbi-blast-2.8.0+\bin\all_nt\nt.60.nsq
C:\ncbi-blast-2.8.0+\bin\all_nt\nt.nal 

when i do:ls /path/blastdb/nt.nal 
example

C:\ncbi-blast-2.8.0+\bin\all_nt\nt.nal

Thank you for the time

[h.mon]

ah, windows... Are you using cmd.exe or the linux subsystem for windows?

[anasofiamoreira94]

sorry, i wasn't clear, im using cmd.exe

[h.mon]

First, try:

blastn -query sample.fasta -db C:\ncbi-blast-2.8.0+\bin\all_nt\nt  -task megablast -outfmt 6 –max_target_seqs 10 > Resultado.txt

or:

    blastn -query sample.fasta -db C:\ncbi-blast-2.8.0+\bin\all_nt\nt.nal  -task megablast -outfmt 6 –max_target_seqs 10 > Resultado.txt

But don't do bioinformatics on cmd.exe, use the linux subsystem for windows, or use linux - the later, in my opinion, is the best alternative.

[anasofiamoreira94]

thanks you so much for the help!

[GenoMax]

Are you actually using /path/blastdb/ in your command like shown above? /path/blastdb/ was a dummy example that @h.mon showed in the answer. You need to replace that with a real path on your own machine.

[anasofiamoreira94]

i have my real path their, of course. i put it their to exemplify my error.