Believe it or not, full, proper annotation of the Olympia oyster genome is nearly complete! Here’s where it stands:
After getting through the initial MAKER annotation and SNAP gene predictions, and then renaming the sequences, I needed to run BLASTp on the FastA file produced by MAKER id mapping in order to assign functionality to the predicted genes.
Continuation of genome annotation of the Olympia oyster genome. Determined initial gene models using MAKER with two rounds of SNAP, relabeled with more user-friendly names, and then performed protein-level annotations using BLASTp. Next, I’m going to run InterProScan5 (IPS5) to help functionally characterize the O.lurida proteins ID’d by MAKER. Once this is complete, I’ll use MAKER to incorporate the IPS5 and BLASTp results into a much more neatly (i.e. human-readable) annotated genome!
After getting through the initial MAKER annotation and SNAP gene predictions, I needed (wanted?) to simplify annotation names that will be easier to read and are in a more standardized format; similiar to NCBI.