Issues while running blastx

Question

[Foad]

Hi,

I face this problem when I run blastx command in linux.

blastx -db ~/Downloads/uniprot_sprot.dat -query ../../../trinity_out_dir.Trinity.fasta -num_threads 2 -max_target_seqs 1 -outfmt 6 > balstx.outfmt6

Warning: [blastx] Examining 5 or more matches is recommended
BLAST Database error: No alias or index file found for protein database [/home/foad/Downloads/uniprot_sprot.dat] in search path [/home/foad/NGS-Book/Chapter2-RNA/Denovo_analysis/Firststep/Blast::]

Thanks in advance!

Foad

[GenoMax]

~/Downloads/uniprot_sprot.dat

dat files are not blast index ready. You should download the fasta format file and create your own blast indexes using makeblastdb.

[Foad]

According to your explanation, i downloaded fasta file and then i used the makeblastdb command, after executing the command, a series of files will be generated. I use either of these in the blastx command, but I still get the same error as before in blastx.

makeblastdb -in uniprot_sprot.fasta  -dbtype prot



uniprot_sprot.fasta.pdb uniprot_sprot.fasta.pin  uniprot_sprot.fasta.psq  uniprot_sprot.fasta.pto
uniprot_sprot.fasta.phr  uniprot_sprot.fasta.pot  uniprot_sprot.fasta.ptf

[Istvan Albert]

you need to show the commands you are using, give the root to the names not the full file name

when blast says you don't have a database - it ALWAYS means one of these:

1. you don't have a blast database or
2. the path the the database is incorrect

Answer 1

[Istvan Albert]

As the blast error says, the name of the blast index is incorrect.

ensure that you are using the correct database name