Question: How to define blast online to filter out PREDICTED and hypothetical proteins
gravatar for hodayabeer
6 weeks ago by
hodayabeer10 wrote:

Hi, I am trying to blast some proteins using 'blastp' vs. some organisms using the Non- redundant protein sequences database (nr)

I have found a solution that is applicable only for blastn by using an Entrez Query of: all[filter] NOT predicted[title] but unfortunately it doesn't work and I still get as a result the 'PREDICTED' proteins.

I will be glad to hear if someone has a solution to that.

Thank you in advance

blastp • 141 views
ADD COMMENTlink modified 6 weeks ago by Mensur Dlakic480 • written 6 weeks ago by hodayabeer10

It would be easier to simply do the blast as usual and then filter the bits you don’t want out of the text result file after the fact.

ADD REPLYlink written 6 weeks ago by jrj.healey13k

Perhaps you can add use the option to exclude the XM/XP models? If this is a computationally expensive search, you may just want to stick to the solution of jrj.healey and filter the results after the fact. That way, if you ever need the entire result set, you can always go back to it without having to run the search again.

ADD REPLYlink written 6 weeks ago by vkkodali1.1k
gravatar for Mensur Dlakic
6 weeks ago by
Mensur Dlakic480
Mensur Dlakic480 wrote:

There is no such option for NCBI's blast to filter out predicted proteins. You may have to download the NR database, remove the proteins you don't want, and perform local BLASTp searches.

I hope you realize that many proteins have words predicted and hypothetical in their annotations without actually being predicted or hypothetical proteins. Also, some proteins would have few or no matches against a database devoid of predicted and hypothetical proteins.

ADD COMMENTlink written 6 weeks ago by Mensur Dlakic480
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