Species-Specific Output From Blast -Db Nt -Remote ...
2
1
Entering edit mode
11.9 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 • 7.2k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
3
Entering edit mode
9.6 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
ADD COMMENT
0
Entering edit mode

How about if more than one species.

Thanks

ADD REPLY
2
Entering edit mode
11.9 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 ...
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 2398 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6