I'm using the C++ version of blastn, with -db nt and -remote. I need to limit my search to a specific organism. I've had success using -gilist <file> to do this on searches with a local database, but that option is excluded for remote searches. Should I use a script to filter the search results, like -gilist, or is there an easier way?
Question: Species-Specific Output From Blast -Db Nt -Remote ...
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kevin.l.neff • 280 wrote:
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chris.mit7 • 60
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8.6 years ago by
kevin.l.neff • 280
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chris.mit7 • 60 wrote:
Add -entrez_query "Homo Sapiens[Organism]" to your search or whatever organism you want.
Such as:
blastn -remote -db nr -query stuff_to_search.fasta -entrez_query "Homo Sapiens[Organism]" -evalue 1e-20 -num_alignments 10 > stuff_to_search.blastn
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Paulo Nuin • 3.7k wrote:
Use the -gilist option in the command line. Create a file with the GIs you want, for instance all bacterias, all mammals, one frog, one lizard, etc and call that file using the option
... -gilist prots.txt ...
Sadly, this doesn't work with -remote option.
How would you generate this gi list for an entire genus or other taxonomy?
Best option would be to go to NCBI website and browse via Taxonomy. This way it is possible to go down/up the tree and check the GIs, as mostly there's one set be genus, species, etc.
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I would also like to know this, but for local blast vs nr!