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Using Abinitio.Pep file vs Pep.all - Annotating using Maker

Greetings,

I am annotating a genome using Maker and have run into an interesting situation. I have a previous annotation of my working bird species which is pretty old. I am updating it using its previous annotation as well as the well documentated Zebra Finch data. I have noticed that there are two files on the Ensembl database for the protein structure - Abinitio and Pep.all.

I noticed that the Abinitio is larger, logicallly it has more data but I am not familiar with the difference between the two file types. What does Abinitio contain that pep.all doesnt? Any suggestions would be appreciated.

maker snp annotation abinitio
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written by ggman ggman

You can find out pretty good explanation about the same reported in README file provided in the same FTP directory which you have mentioned in your question. OR here is the link for README file.

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written by Nitin Narwade Nitin Narwade

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