Annotation of Syngnathus typhle

GeneMark-ESv2.3e was run onthegenomeassemblyandSNAPv20131129 onthegenesfoundby
CEGMA.MAKERv2.31 usedthetrainedgenepredictors,aTrinity
transcriptome assembly, all repeats in RepBase as called by MAKER and
proteinsfromUniProtKB/SwissProtr2014_9 forafirstpass annotation
ofthegenomeassembly.TheresultofthefirstpasswasusedtoretrainSNAP
andtrainAUGUSTUSv3.0.2 andaseconditerationwasperformedusing
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
informationwastransferredtoalloutputofMAKER.Thisannotated19,668gene
models. InterProScan was run on thepredictedproteins of theseandgene
nameswereallocatedbasedonmatchwithproteinsinUniProt/SwissProt.
The files starting with Syngnathus_typhle is a more recent annotation done with Funannotate. The files starting with syty is the MAKER annotation

GeneMark-ESv2.3e被应用于基因组组装序列，同时使用SNAPv20131129对CEGMA鉴定得到的基因进行分析。MAKERv2.31利用已训练的基因预测工具、Trinity转录组组装结果、MAKER自身识别的RepBase重复序列，以及UniProtKB/SwissProt r2014_9版本的蛋白质序列，对基因组组装序列开展首轮注释。首轮注释的结果被用于重新训练SNAP模型，并训练AUGUSTUSv3.0.2模型，随后采用相同配置开展第二轮注释迭代。将MAKER最终输出的蛋白质序列与UniProtKB/SwissProt数据库中的蛋白质序列进行BLAST比对，并借助InterProScan v5.4-47对这些蛋白质序列的结构域进行分类。上述分类信息被整合至MAKER的全部输出结果中，最终完成了19668个基因模型的注释。再次对上述基因模型预测得到的蛋白质序列运行InterProScan，并基于与UniProt/SwissProt数据库中蛋白质的比对结果为基因分配官方名称。以Syngnathus_typhle为前缀的文件为采用Funannotate工具完成的最新注释结果，而以syty为前缀的文件则为MAKER注释结果。