[susanklein]

If you want to limit to a specific taxon, you can use the the entrez_query parameter, e.g.:

blastn -db nt -entrez_query txid5693 -remote -query <(echo CTTTTTTTTCTTTTTTTAAAAGTTTTTGAAAAAAGGAAAAAGAAAAATTTTCTTTAGGTTGGGATGTGATTTTATT)

-Keith

well, that certainly makes things easier. I can't test it at the moment, does it work on a local db, and with blastx??

thanks

S.

[khughitt]

It should work the same with blastx, but is limited to remote searches.

[susanklein]

oh, ok, thanks, but remote search far too slow with large numbers of queries.

[khughitt]

Ah, okay. In that case I'm not really sure what the best approach would be -- just starting to experiment with the command-line interface myself and haven't set up any local databases yet.

Goodluck!

[cliffbeall]

Sorry, late to the party here but I was googling the error:

BLAST Database error: BLASTDB alias file creation failed. Some referenced files may be missing

trying to restrict blastn searches of refseq_genomes to bacterial sequences with a gi list.

I think this might be a bug in the blastdb_aliastool (2.6.0+). Although it failed to make an alias, I could use the gi list that it made to restrict blast in the command. It created a file called (in my case) refseq_bact_genomes.n.gil before failing on the alias, and I ran blastn with -gilist that file and it worked (it did need a lot of cpu and memory - up to 5 hrs and 110 GB memory).