Unipro UGENE Online User Manual v. 1.14.0
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Search timeout — sometimes a database doesn’t respond, therefore you need to re-wait for the response. This option sets the time that will be spent for re-appeal to the database. Note that in case of long sequences time for request preparation increases and the search takes several minutes.

Tip

There is a little difference in default values of parameters between NCBI Nucleotide BLAST web interface and UGENE:

  • The web interface uses the megablast option by default: the search is fast, but only highly similar sequences are found.
  • UGENE ignores the option by default: the search may take more time, but all somewhat similar sequences are found.

Check the Megablast option, if you want exactly the same results to be found in UGENE as you had in the NCBI web interface.

 

Also there is Advanced options tab:

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