benchmark blastp

[Mai Said]

I am working on a research about blastp. I wanted to run the benchmark that exists in the path ftp://ftp.ncbi.nlm.nih.gov/blast/demo/benchmark/ and I was wondering where can I find the original fasta benchmark database file before makeblastdb was run and I could only find the nr file in the db/fasta directory ftp://ftp.ncbi.nlm.nih.gov/blast/db/fasta but not the subset benchmark. Will you please guide me to where I can find the benchmark fasta file.

[GenoMax]

All the information you need (queries, database etc) is in the tar file: ftp://ftp.ncbi.nlm.nih.gov/blast/dem...ark2013.tar.gz

[Mai Said]

The tar file contains the preformatted database files but I need the database before formatting because I want to call makeblastdb with sorting option to sort database sequences

[GenoMax]

You can extract sequences from the pre-formatted database by doing the following:

$ blastdbcmd -db ./benchmark.aa -entry all -outfmt '%f' > protein_seq

$ blastdbcmd -db ./benchmark.nt -entry all -outfmt '%f' > nuc_seq

[Mai Said]

Thank you so much. I am using this benchmark for psiblast not blastp. Do you know any benchmark for psi.