Question: How To Set Own Protein Fasta File As Database In Ncbi-Blast-2.2.28
0
gravatar for Nari
5.4 years ago by
Nari870
United States
Nari870 wrote:

I have installed NCBI-Blast-2.2.28 on win-7.
Also set the path variable to bin directory. I want my protein fasta file to be used as database. against protein query with few sequences. (all vs all).

Upon following commands:

 blastdbcmd -db my_db.fasta  -outfmt "%f" -out query.fasta.txt

 blastp -query query.fasta -db my_db.fasta -out output.txt

Error: No alias or index file found for protein database

(files are present in folder specified).

Where I might have gone wrong?

• 3.5k views
ADD COMMENTlink modified 5.4 years ago by Michael Dondrup46k • written 5.4 years ago by Nari870
1
gravatar for Michael Dondrup
5.4 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

You should read the fine Blast+ documentation. you need to run makeblastdb to format a database first. You can't use blastdbcmd on a fasta file. You can use blastp with -subject my.fasta instead of -db.

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by Michael Dondrup46k
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