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Old 04-01-2011, 11:51 AM   #1
d f
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Location: MN

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Default 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
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Old 04-03-2011, 08:00 PM   #2
kokonech
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Default

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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Old 04-04-2011, 09:09 AM   #3
d f
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Thanks! I'll look into UGENE.

d f
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Old 04-04-2011, 09:48 AM   #4
joscarhuguet
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You could try Artemis.

http://www.sanger.ac.uk/resources/software/artemis/
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Old 01-06-2017, 05:33 PM   #5
ndunn
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Default 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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Old 01-06-2017, 07:47 PM   #6
Brian Bushnell
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Interesting that Greek gods are so involved with annotation...
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Old 01-07-2017, 02:42 PM   #7
Margaret64
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Artemis is one of the best in my opinion. You should check it out.
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