GeneMark-ES v2.3e was run on the genome assembly and SNAP v20131129 on the genes found by
CEGMA. MAKER v2.31 used the trained gene predictors, a Trinity
transcriptome assembly, all repeats in RepBase as called by MAKER and
proteins from UniProtKB/SwissProt r2014_9 for a first pass annotation
of the genome assembly. The result of the first pass was used to retrain SNAP
and train AUGUSTUS v3.0.2 and a second iteration was performed using
the same set-up. The protein sequences from final output of MAKER were
BLASTed against the UniProtKB/SwissProt proteins and InterProScan v5.4-47 was used to classify protein domains in the protein sequences. This
information was transferred to all output of MAKER. This annotated 19,668 gene
models. InterProScan was run on the predicted proteins of these and gene
names were allocated based on match with proteins in UniProt/SwissProt.
The files starting with Syngnathus_typhle is a more recent annotation done with Funannotate. The files starting with syty is the MAKER annotation