The Remote BLAST plugin provides the capability to annotate sequences with information stored in remote databases.
To perform a remote database search open the Sequence View, select the sequence region to analyze and click the Analyze ‣ Query remote database context menu item. If a region is not selected the whole sequence will be analyzed.
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When a sequence is translated the translation table from the active Sequence View is used. Finally, all 6 translations are used to query the remote database with the selected blastp or cdd search.
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You can see the description of the annotation saving parameters here.
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.
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