Question: Species-Specific Output From Blast -Db Nt -Remote ...
1
gravatar for kevin.l.neff
4.2 years ago by
kevin.l.neff100
Mayo Clinic College of Medicine
kevin.l.neff100 wrote:

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 • 2.9k views
ADD COMMENTlink modified 24 months ago by chris.mit760 • written 4.2 years ago by kevin.l.neff100

I would also like to know this, but for local blast vs nr!

ADD REPLYlink written 4.2 years ago by Lee Katz2.7k
3
gravatar for chris.mit7
24 months ago by
chris.mit760
United States
chris.mit760 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

ADD COMMENTlink written 24 months ago by chris.mit760

how about if more than one species.

thanks

ADD REPLYlink written 14 months ago by Manoj10
2
gravatar for Paulo Nuin
4.2 years ago by
Paulo Nuin3.7k
Canada
Paulo Nuin3.7k 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 ...
ADD COMMENTlink written 4.2 years ago by Paulo Nuin3.7k

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

ADD REPLYlink written 4.2 years ago by kevin.l.neff100

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

ADD REPLYlink written 4.2 years ago by Paulo Nuin3.7k

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

ADD REPLYlink written 4.2 years ago by Lee Katz2.7k

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.

ADD REPLYlink written 4.2 years ago by Paulo Nuin3.7k

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...

ADD REPLYlink written 4.2 years ago by kevin.l.neff100
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