We recently annotated two EM phages. The auto-annotations for both produced many many false positive genes. We saw reverse genes without BLAST hits without much coding potential completely overlapping forward genes with good CP and BLAST hits. We had to delete nearly half of the auto-annotated genes.

Debbie added: Note when you review this in DNA maser, you will find the GeneMark has called all of the forward genes and Glimmer has called all of the reverse genes. this is based on how these 2 programs call this differently OR is it because there is a big open reading frame in the same location and the programs discriminate which one to pick differently. If you simply discard one of the sets of data, are you discarding possible genes. if all of these genes are in PECAAN, always good to see if you are throwing away anything with a functional….
Edited 06 Jun, 2023 02:05
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