Annotation of Syngnathus typhle

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.