How to export BLAST results in csv format

The results of a BLAST search can be displayed as either a Hit Table or a Query Centric alignment.  To export the results of a single Hit table (ie the results of a single BLAST search), select all the entries in the document table that you wish to export and selecting File -> Export -> Selected Documents


Choose to save this file in .csv format, and specify a name for the file. This will then bring up a menu that allows you to select which columns from the table you want to be exported into this file.


Select the fields you wish to export, then select OK to export the file.

For exporting the results of a batch BLAST in a single table, you should instead select Query-centric alignment only under Results when you set up the BLAST search.  


This will return one alignment per query, and you will see that all of the hits in the alignment have a Search Hit annotation on them containing details about the BLAST hit, such as the description, E Value and % identity.   You can use the Annotations table to export all of this information for all queries in a single CSV file. 

Select all the alignments that are returned and you will see a table of results at the bottom of the sequence viewer.


Select Types -> Show One -> Search Hit to only display your BLAST search results in the table. The  Columns button will allow you to add and remove columns to display values like % Pairwise Identity and E values.  Once you have altered this table to reflect the details you wish to be exported, you can then export this table in .csv format by clicking the Export Table button.  


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