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|04-01-2011, 11:51 AM||#1|
Join Date: Feb 2010
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!
|04-03-2011, 08:00 PM||#2|
Location: Berlin, Germany
Join Date: Sep 2010
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,
|01-06-2017, 05:33 PM||#5|
Location: Eugene, OR
Join Date: Apr 2013
If your data is in GFF3 + FASTA for the reference sequence you can use Apollo
|annotation, gene prediction, genome browser, gmod, transcript prediction|