Entering edit mode
3.3 years ago
Vasiliy Krestov
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30
My group investigates a family of proteins. We need to get all members of this family which are in NR database. In the past, my colleagues made it by 5 iterations of psi-blast against NR. This data is outdated and now and we need to renew it.
My question is general. Is it possible to make all this by psi-blast from blast+ without downloading the whole nr on a server? 
If you want to use psi-blast locally, yes, I think that you will have to download the NR database... Perhaps it will be easier to use psi blast online ?
Thanks for your answer!
I've tried this but after 3 iterations the result page freeze and it's hard to make it respond, somehow I managed to launch a 4 iteration but after several seconds it redirected me to the blastp home page. I think it behaves like this because It finds a lot of proteins I set a threshold on 20000 sequences (it's a maximum of the web psi-blast) and blast did find a lot of proteins. I asked a friend of mine to try this from his computer and he also got this problem.
With this query I got this problem. Would you like to try it?
I see, the interface becomes also sluggish for me after the second iteration when there are a lot of sequence shown... Perhaps you could try to lower the 20000 max-targets threshold or increase the percent identity/evalue threshold. Or build the NR database locally.