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

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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.

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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.  

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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.

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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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