Question: Multiple Psi-Blast Iterations From Command Line Using Remote Database
1
gravatar for jdromano2
6.9 years ago by
jdromano210
Burlington, VT, USA
jdromano210 wrote:

When using PSI-BLAST from the command line, it does not allow you to specify successive iterations if the protein sequence database is on a remote server (i.e., using the '-remote' flag). I'm working on a bioruby script in which I need to iterate on PSI-BLAST until there are no new sequences added, but I need to use the remote nr database on NCBI's servers.

Is there a quick and easy way to get it to do these iterations for me without having to manually parse the results of PSI-BLAST and then using the results in a new PSI-BLAST call?

pssm blast • 2.5k views
ADD COMMENTlink written 6.9 years ago by jdromano210

Hey, did you ever figure this out? (Not even sure if you're still on this website anymore) I'm working on the exact same problem. Thanks.

ADD REPLYlink written 3.4 years ago by rwipfle20

Hey, did you ever figure this out? (Not even sure if you're still on this website anymore) I'm working on the exact same problem. Thanks.

ADD REPLYlink written 2.4 years ago by rosemont0
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