Question: Is It Possible To Use Blast+ To Hit Embl Database?
gravatar for ramesh.8v
5.0 years ago by
United States
ramesh.8v200 wrote:

I am having nightmare in using NCBI-BLAST+ for last two weeks. Now blasting remote database became very slow irrespective of my computer or my internet connectivity speed. I am thinking to use EMBL-EST database instead of NCBI-EST database as an alternative. Is it possible to hit EMBL-EST database using BLAST+ tool? Specifying organism specific database like est_others will really increase the speed?
Many thanks!

blast+ • 1.1k views
ADD COMMENTlink modified 5.0 years ago by Torst900 • written 5.0 years ago by ramesh.8v200
gravatar for Torst
5.0 years ago by
Torst900 wrote:

It is possible you have been throttled by ENA for using the web service too much.

NCBI have explicit guidelines on this:

Do not overload the NCBI servers. If you are intending to perform more than 20 searches in a session you should comply with the following guidelines:
1.) Do not contact the server more often than once every three seconds.
2.) Do not poll for any single RID more often than once a minute.
3.) Use the URL parameter email, and tool, so that we can track your project and contact you if there is a problem.
4.) Run scripts weekends or between 9 pm and 5 am Eastern Time weekday if more than 50 searches will be submitted.

You should just download the BLAST+ binaries and the preformatted EST databases and run the searches locally?



ADD COMMENTlink written 5.0 years ago by Torst900

I already tried these, but I still get the same problem :(.

ADD REPLYlink written 5.0 years ago by CuteDriving6630

Downloading and using pre-formatted database is an useful alternative :)

ADD REPLYlink written 5.0 years ago by ramesh.8v200
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