[maker-devel] How to evaluate the results of gene prediction

[陈文博]

Hi All,

I am using MAKER to annotate a insect genome. Firstly, I trained Augustus
and GeneMark-ET outside of Maker using aligned RNA-seq data. Then, I gave
them to Maker. The evidences included assembled RNA-seq data, protein
sequences of my insect, proteome sequences of three related insects and
Swiss-Prot. At last, I used the gene models generated by Maker with AED <
0.01 to train SNAP for two rounds. So my questions are:

1. how to evaluate the results of ab initio training. How can I know these
gene finders were well trained?

2. Should I add EST evidences? How does Maker work on the locus where there
is only partial EST evidence? Will the partial EST sequences cause gene
models to be partial?

3. Is there some gold-criteria to evaluate the results of gene prediction?
How to improve it?

Thank you!

Best regards,
Wenbo
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