[maker-devel] coordinates re-mapping question

[Bob Freeman]

Carson et al.,

I seem to recall a note from you or a note hitting this list that  
MAKER can handle remapping coordinates. How does one go about doing  
this??

Our situation: we obtained gff3 output from AUGUSTUS (independent of  
MAKER) for gene models from a 1.0 assembly of our genome. Our current  
GBrowse installation is on the 1.0 assembly, and I've loaded this, the  
gff3 data, as well as nt and protein versions of the models into  
GBrowse.

A v1.1 assembly is now available; although there have been changes to  
remove contaminating sequences, I'm not sure how different the  
assemblies are. But I need to re-map the 1.0-based gene models onto  
the 1.1 assembly.

How do I proceed with this? Again, I have gff3 output, as well as nt  
and protein fasta files that I generated using the gff3 output.

Thanks much!
Bob

-----------------------------------------------------
Bob Freeman, Ph.D.
Acorn Worm Informatics, Kirschner lab
Dept of Systems Biology, Alpert 524
Harvard Medical School
200 Longwood Avenue
Boston, MA  02115
617/432.2293, vox

The only other person I've apologized to is my mother and that was  
court ordered.
	-- Karen Walker from Will & Grace



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