Species-Specific Output From Blast -Db Nt -Remote ...
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10.8 years ago
kevin.l.neff ▴ 340

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?

blast • 6.7k views
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I would also like to know this, but for local blast vs nr!

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8.5 years ago
chris.mit7 ▴ 60

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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How about if more than one species.

Thanks

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10.8 years ago
Paulo Nuin ★ 3.7k

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 ...

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Sadly, this doesn't work with -remote option.

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Yes, you are right. IMHO, you would be best to download the nr DB and run locally.

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How would you generate this gi list for an entire genus or other taxonomy?

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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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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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