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Good annotation editor?

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  • Good annotation editor?

    I am seeking a good annotation editor. I have genes predicted by ab initio and RNA-seq gene/transcript predictors, but many of the predictions need to be fixed by hand. I am seeking an easy way to do that.

    Does anyone have any suggestions for useful and easy-to-use (and easy-to-install) annotation editors?

    It would be helpful if the annotation editing software has these features:

    * genome browser so I can examine the genes against the reference genome

    * reads in and writes out the annotations from a standard genome annotation format like gff3, gtf, or bed.

    * allows me to change the annotations easily, preferably using the mouse. For example,
    - shorten or lengthen exons
    - eliminate or add exons
    - change the splicing
    - add UTRs

    * saves the changes in a way that I can backtrack and look at past changes

    * allows the option to add notes as to why changes were made

    * writes out a FASTA file of the sequences of the edited annotations

    I've looked a bit at Apollo. To edit annotations, I have to use a Chado XML or GAME XML format. I don't know how to get my automated annotations, which are in gff3, into those formats. If Apollo is a really good editor, I would consider making the effort to get my data into Chado or GAME.... Anyone have any comments about using Apollo?

    Any suggestions/comments would be helpful!

    d f

  • #2
    There is an open source genome analysis suite called UGENE. You should give it a try. It has a lot of capabilities to manage annotations.

    From your wish-list it supports the following features:
    - genome sequence and annotations visualization
    - import and export of annotations in gff format
    - allows to easily modify annotations. For example, to change the location you select annotation, press f2 and change it parameters in appeared dialog.
    - allows to add notes
    - allows to export sequences of selected annotations
    Although UGENE lacks changes back tracking and doesn't support changing the annotations with mouse, you can contact the developers team with a feature request. In most cases it will take relatively short time for the feature to be implemented.

    Hope that helps,


    • #3
      Thanks! I'll look into UGENE.

      d f


      • #4
        You could try Artemis.


        • #5
          If your data is in GFF3 + FASTA for the reference sequence you can use Apollo

          If your data is in GFF3 + FASTA for the reference sequence you can use Apollo. If you are already using JBrowse (, you just point to the directory and away you go.


          • #6
            Interesting that Greek gods are so involved with annotation...


            • #7
              Artemis is one of the best in my opinion. You should check it out.


              • #8
                Here is


                • #9
                  great i will use it too. If your website undergoes any quite issue, your application are going to be in trouble too. Don’t assume that your web app will work perfectly if you don’t have a top quality corporate website. I reocommend to test also this service For instance, if the web site’s URL takes a while to load or if uncomfortable ‘cookies’ show up when entering the website, accessing it through the appliance will entail an equivalent issues.
                  Last edited by kabutokey; 07-09-2022, 01:36 AM.