How to search and filter in Geneious Prime

Geneious Prime 2020 has a new improved search interface enabling you to easily find documents, folders and operations within Geneious.  

To start a search, click on the Search box at the top right of the Geneious screen, or use the shortcut keys Shift-cmd/cntrl-F.   When you first click on the search bar, you'll see a list of the last documents and folders you opened, enabling you to quickly access your recently browsed files.


As you start typing in the search bar, matching results will be updated in real time. By default, all folders in both local and Shared databases will be searched. To restrict search results to the current folder, change the Search setting from ”Everywhere” to ”This folder”. The Match option enables you to choose between searching all fields or just the document name. These settings will be remembered until the search window is exited.  



Advanced Search

For more searching options on documents within the selected folder, such as searching for specific terms in particular document fields, or searching by multiple criteria, click Advanced Search in "Selected Folder"and then click the More Options button.  


Document fields to search in can be selected in the left-most dropdown menu, and options for restricting the search can be selected in the middle menu.  To search in more than one field, or with more than one search term, click the + button, and specify whether you want to match All or Any of the terms at the top of the search window.


For more information on Advanced search options, see section 4.2.1 of the Geneious user manual.  



Geneious Prime 2021.1 onwards includes a quick filter option above the document table. filter32.png

To use, click the filter icon and type in the text you are searching for. Geneious will display all documents in the table that match this text and hide all other documents. To go back to viewing all documents, clear or close the filter box.



This option can also be used for filtering on-the-fly while searching public databases such as NCBI. Type in the appropriate text in the filter box and only those documents that match both the original criteria (as specified by the search terms) and the filter text will be displayed.


Searching for Geneious operations

If you can't remember where a particular operation or tool is located in the Geneious menus, type it into the search bar and Geneious will show you where it is located under Actions. This can also be useful for finding particular Workflows.  


Under Actions you'll see on the right where each operation is located in the Geneious menus.   Click on the result to open the options dialog for that operation.  


Searching within a document

To search for a specific motif in your sequences, annotations or sequence names within a particular document, click the Find in "Selected Document" option in the search bar.  This opens the Find in Document option which can also be accessed via the Edit menu or the shortcut key cmd/cntrl-F.  Matching regions will be selected in the document once the search has finished.  


An alternative way to search for sequence motifs in a document is to use Find Motifs under the Annotate and Predict menu.  Find motifs has additional options for allowing mismatches and PROSITE-type patterns in the search.  Matching motifs are annotated on the sequence.   





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  • Avatar
    Dylan Maddox

    I like the new search function when I'm trying to find something I've lost, but it kills the ability to filter files quickly in a particular folder, which is the main reason I use the search bar. Previously, one could limit the files visible by simply entering a search term. The new search provides the search results in a new window that you can interact with if you select the advanced options (why this is an advanced option, I don't have any idea) but the search takes 20-30 seconds to find the names of 3 files in a folder of 10 files. 

    Edited by Dylan Maddox
  • Avatar
    Richard Moir

    Thanks for the feedback Dylan, we have been working on optimizing the speed of simple filters for 2020.2.3 which is due out soon. Please update when that comes out and you'll hopefully see an improvement.

    We acknowledge that the new search design is not as good for filtering in a folder. We will continue working on improvements to hopefully get the best of both worlds.

  • Avatar
    Niloofar Vaghefi

    I agree with Dylan. The ability to filter quickly and in real time, which I used to implement very often, is now killed. I have the 2020.2.3 version now and still cannot use the search box for filtering as I used to. I now just sort everything by name and do a search by eye, which is much much faster than the search function. Is it possible to have the Filter function back?