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?
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written
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kevin.l.neff •
2 answers
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
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.
Yes, you are right. IMHO, you would be best to download the nr DB and run locally.
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.
Yes, I agree. However, my web server only allows 10 GB data, so I need to come up with an alternative. Dreamhost or some other service may be the easiest solution, but I wondered if there was a way to do this without bringing in the big guns. Seems like no...
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