Using psi-blast to obtain all members of the protein family
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10 weeks ago

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 This data is outdated and now and we need to renew it.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? This image It seems to me that the user can't define several options when using ncbi severs. Do I understand right that the only way to solve this problem is to download nr and make all manipulations on a local server? Thanks :)

psi-blast blast • 270 views
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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 ?

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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.

query FYRAQETALALLRLDGAQGWPEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRK AKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAK AGLQVVALSGAYPAELAVGFDAGGRESFRFGGAACAVGGDGGHLLWTLPEAQAGERIPQE VVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALEALAREGIAYDLVSVRKSG GGRVYPVQGRLADGLYVPLEDKTFLLLTVHRDFRGTPRPLKLVHEAGDTPLEALAHQIFH LTRLYPASGFAFPRLPAPLHLADRLVKEVGRLGIRHLKEVDREKLFFV

With this query I got this problem. Would you like to try it?

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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.

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