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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,
    Konstantin

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

      d f

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      • #4
        You could try Artemis.

        http://www.sanger.ac.uk/resources/software/artemis/

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        • #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 (jbrowse.org), you just point to the directory and away you go.

          http://genomearchitect.org/

          https://github.com/gmod/apollo

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

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

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