[maker-devel] Question about adding UTR

[Carson Holt]

MAKER will automatically try and build the UTR if it can determine the UTR from the EST data, so you should focus on  getting the ESTs themselves to be longer as you eluded to.

The add_utr_gff just explicitly labels UTR in the GFF3 file.  UTR is implicit in the GFF3 specification (i.e. exon region without CDS overlap), but some programs require explicit UTR statements for the UTR, so we provide a script to add those.

Thanks,
Carson


On 2/3/10 11:09 AM, "Shane Brubaker" <SBrubaker at Aurorabiofuels.com> wrote:

Hi, I was wondering if someone could give me a little background on extending gene models to include more UTR.  I see a script called add_utr_gff.pl, but I'm not entirely clear on what this does.

Basically we have made gene models using MAKER and these were fed ESTs that come from NGS data, assembled using Velvet.  But we often see transcription that goes outside the boundaries of the gene.  When we do quantitative analysis of transcription using Cufflinks, we do not always get results as accurate as we would like, because part of the UTR is not in the gene model.

So I guess I'm wondering, does MAKER by default use the entire EST, and extend the gene model to include UTR?  If so then my main problem might be getting the ESTs themselves to be longer.

And what does add_utr_gff do, and do I need to use that?

What is the current status of plans for direct use of NGS data by Maker?


Thanks so much for your help!

- Shane



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