How to get Pseudogene

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How to get Pseudogene
Dear sir:
    I'd like to mask some pseudogene to my annotation. How can I do it?
    In the guide, the first step is 
  • "Run a tblastn of the protein sequence (query) vs. the intergenic genome sequence (subject/database)"

    My question is:
  1. What do the " protein sequence and  the intergenic genome sequence " refer  to seperately? My own protein database?
  2. How to use the result in maker annotation?
    Best wishes!

Chao Chao


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