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Old 06-19-2015, 07:26 AM   #1
Mai Said
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Default benchmark blastp

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.
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Old 06-19-2015, 08:23 AM   #2
GenoMax
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All the information you need (queries, database etc) is in the tar file: ftp://ftp.ncbi.nlm.nih.gov/blast/dem...ark2013.tar.gz
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Old 06-19-2015, 08:41 AM   #3
Mai Said
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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
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Old 06-19-2015, 08:50 AM   #4
GenoMax
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You can extract sequences from the pre-formatted database by doing the following:

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

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

Last edited by GenoMax; 06-19-2015 at 08:52 AM.
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Old 06-19-2015, 08:53 AM   #5
Mai Said
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Thank you so much. I am using this benchmark for psiblast not blastp. Do you know any benchmark for psi.
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