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.
-
-
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
-
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
-
Thank you so much. I am using this benchmark for psiblast not blastp. Do you know any benchmark for psi.Comment
-
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment