The GO terms, functional descriptions, and other annotations are from the Pannzer annotation online server  [Annotate Tab](http://ekhidna2.biocenter.helsinki.fi/sanspanz/) using the default settings on the protein sequences from the MaizeGDB download site (https://download.maizegdb.org/).

Genomes annotated: B73 versions RefGen_v3, RefGen_v4 and RefGen_v5, A188, Mo17 (CAU), W22, and the 25 NAM genomes.

Text outputs are available for downloading. The downloadable file named "_GO.out" and "_DE.out" contain intermediate results for each protein. The final results are in the "annotations (.out)" file. It is a parseable file, which uses a context sensitive grammar, as explained below. The file has six tab-separated columns labelled qpid, type, score, PPV, id and desc. The first column (qpid) always contains the identifier of the query sequence. The second column (type) can take the following values, and the score, PPV, id and desc columns change meaning accordingly:

   original_DE: score is euk for eukaryotic query species and bac otherwise; id is the form factor of desc, the description from the input FASTA file
   qseq: desc is the amino acid sequence of the query protein
   DE: score is the prediction score; PPV is the normalized prediction score between 0 and 1; id is the form factor of desc, the predicted description
   GN: desc is the gene symbol. A gene symbol is predicted if its support is greater than half in the list of homologs
   ontology_predictor where ontology is one of MF (molecular function), BP (biological process), CC (cellular component) and predictor is one of RM3, ARGOT, HYGE or JAC. score is the prediction score, PPV is the normalized prediction score between 0 and 1, id is the GO identifier and desc is the short description of the GO class
   EC_predictor: desc is the GO class that has the highest PPV and has a link in ec2go, id is the EC class
   KEGG_predictor: desc is the GO class that has the highest PPV and has a link in kegg2go, id is the KEGG pathway identifier

Toronen P, Holm L (2022) PANNZER - a practical tool for protein function prediction. Protein Science 31, 118– 128. https://doi.org/10.1002/pro.4193

Last update 2/8/2022 - C. Andorf