Is It Possible To Use Blast+ To Hit Embl Database?

Question

[second_exon]

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!

Answer 1

[Torst]

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

NCBI have explicit guidelines on this:

http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo

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?

[CuteDriving663]

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

[second_exon]

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