I have been having some trouble with running command line BLASTn remotely. Therefore, upon recommendations, and considering I have >100 searches planned, I am considering just downloading the nt database (thankfully possible).
My issue is that one of the settings that proved valuable with my data in WebBlast is running an Entrez query. I get more useful results for each query when instead of one search, I run three, with each of the sub-searches delimited by subject sequence length (e.g.
-entrez_query 700:1000[slen] to only get the results which are between 700 and 1000 nucleotides long).
WebBlast and remote Blast have that, local Blast does not.
Since I only really need 2 Entrez queries, I guess it would not be conceptually impossible to get my copy of nt database as FASTA, and then run a script to split it into three directories (700-1000nt, 1000-1400nt, the rest while discarding all<700 nt), then make three blastable databases out of it. However it does feel rather inelegant. I was wondering if anyone might have a better solution!