How To Set Own Protein Fasta File As Database In Ncbi-Blast-2.2.28
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?
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Michael Dondrup
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Naren
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Naren
1 answer
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.
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