[maker-devel] Speaking of AED...

[Daniel Ence]

Hi Professor Hu, 

 I’m excited that you’re teaching from this review. I hope that you find it useful for your class! 

Annotation 1 has an AED of 0.2 and not 0 because the middle exon doesn’t line up exactly with the evidence alignments. Since there are bps in the annotation that aren’t supported by evidence, then it has an AED of > 0. It’s a little hard to see in the figure, but if you use a straight-edge, you can see it. 

Feel free to let me know whether that helps clear things up.

Thanks,
Daniel


> On Nov 7, 2014, at 11:34 AM, Jim Hu <jimhu at email.tamu.edu> wrote:
> 
> I was teaching Yandell and Ence (2012) in the genomics class I co-teach, and was having trouble understanding the values for AED in Box 4 Figure Bb derive from the evidence set in Figure Ba. 
> 
> Box 4 says: "AAED is caculated in the same manner as SN and SPm but in place of a reference gene model, the coordinates of the union of the aligned evidence (see panel Ba) are used instead". In the union, I expect that a bp that is in an exon in any of the evidence would be considered a TP. If so, then why isn't nt-level AED for Annotation 1 in Bb  zero?
>   
> I'm probably missing something trivial. 
> 
> Thanks
> 
> Jim
> =====================================
> Jim Hu
> Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
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