[maker-devel] How to evaluate maker proteins' quality?

[dcg at cau.edu.cn]

Dear sir:
    After I finished my maker running, I should check the quality of my results.
    My annotation purpose is to find some new proteins.
    There is about 30K reviewed proteins of my species. If I want to see how many predicted proteins can support the reviewed proteins, how to do it?(Can blastp be OK? How to set the threshold? )
    I used Uniprot, ESTs and RNA-seq to do my annotation. From my perspective, if the protein is reviewed and used to train snap/augustus, we should get the same one after several training rounds. So I planned to align maker_proteins to Uniprot proteins(which I utilized to annotate). If the predicted proteins match Uniprot by 100% identity and coverage, they can be thought to support the reviewed proteins. Is it correct?    
    
    If not, maybe I can evaluate my proteins only by AED value and proteome domain?

    I'm looking forward to your help. Thanks a lot!

Yours sincerely!

Chao Chao


dcg at cau.edu.cn
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