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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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All the information you need (queries, database etc) is in the tar file: ftp://ftp.ncbi.nlm.nih.gov/blast/dem...ark2013.tar.gz -
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 sequencesComment
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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, 07:52 AM.Comment
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Thank you so much. I am using this benchmark for psiblast not blastp. Do you know any benchmark for psi.Comment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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