[maker-devel] Pseudogene identification

[Quanwei Zhang]

Hello:

We used Maker2 to annotate a new rodent genome. By using the annotated
genes we did gene family expansion analysis, and found several gene
families under expansion in the new rodent genome. But we want to check
whether some annotated genes are Pseudogenes, which lead to the expansion.
Do you have any suggestions on this?

We found the Maker-P can annotate Pseudogene, but we are not sure whether
it is worth to repeat our annotation with Maker-P. Besides, we are not sure
whether the default parameters of Maker-P are good for a rodent species.
What's more, in my understanding the Maker-P will identify Pseudogenes in
the intergenic spaces (which I think the annotated coding genes will be not
be tested and checked).

Do you have any suggestions to solve our problem? We do not want to
identify Pseudogene on the genome wide, but only want to check those genes
showing expansion (to make sure all those gene copies really function).

Many thanks

Best
Quanwei
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