How to use a downloaded BLAST database
I am trying to BLAST some sequences against all the virus and prokaryote genomes available in NCBI. I found out that there are existing BLAST databases for both of them that can be downloaded from BLAST (ftp.ncbi.nlm.nih.gov/blast/db/) I downloaded the virus BLAST database (ref_viruses_rep_genomes) and expanded the compressed file. The resultant folder looks like a legitimate BLAST database, with .nb, .nhr, .nin, .nnd etc files.
When I try to use this database like
blastn -query /.../C1_animal_spacers_nonredundant.fasta -db /Volumes/bam/DRG/PK/annotations/ref_viruses_rep_genomes -outfmt 6 -out /.../spacerBLASTresults/C1_animal_spacer_BLAST_hits.txt
it gives me the error –
BLAST Database error: No alias or index file found for nucleotide database [/Volumes/bam/DRG/PK/annotations/ref_viruses_rep_genomes] in search path [/.../C3_human::]
What may be going wrong? Do I need to somehow let my machine know that this database exists now? Also, the ‘search path’ that is part of the error message is different from either my query location or database location. Not sure whats the reason for that either.
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