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The second run of MAKER was performed using SNAP and GeneMark trained for Oryza sativa in conjunction with Augustus trained for Zea mays.
Both SNAP and Augustus were used as gene predictors in the fourth run of MAKER to produce a final set of gene annotations, which included 6,718 genes encoding 6,771 transcripts.
A subsequent run of MAKER was performed using Genemark and Augustus with the Uniref50 protein database [ 33] and the predicted proteins from A. flavus AF70 and A. parasiticus as evidence of protein homology.
Genome annotation pipelines have been proposed, such as MAKER [ 72] or SABIA [ 85], as well as web prokaryote annotation servers (RAST server at the National Microbial Pathogen Data resource [ 86] and the MicroScope platform [ 87]), but this requires intensive computation resources (indeed, a full run of MAKER can take as long as a few weeks for a prokaryote genome).
An initial run of MAKER was performed to develop a set of genes that were used to train Augustus with predicted proteins from A. oryzae RIB40, A. flavus NRRL 3357 (L-type), A. flavus AF70 (S-type), and A. parasiticus SU-1 with the "protein2genome" option set.
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CEO of Professional Science Editing for Scientists @ prosciediting.com