Genome Annotation

Downloadable File
Organism: 
Seriola dorsalis (Yellowtail Amberjack)
Program, Pipeline Name or Method Name: 
BRAKER, AUGUSTUS
Program, Pipeline or Method version: 
2015
Source Name: 
Seriola dorsalis annotation version 1 in gff3 format
Time Executed: 
09/09/2016
Materials & Methods (Description and/or Program Settings): 
BRAKER (Hoff et al. 2015) was used to annotate the genome using raw RNA-Seq data. BRAKER pipeline uses GeneMark-ET (Lomsadze et al. 2014) to perform unsupervised training using a genome file and the RNA-Seq data. After training, GeneMark-ET creates an ab initio gene set. Those gene structures that have support by RNA-Seq alignments in all introns are selected for automated training of AUGUSTUS (Stanke & Waack 2003). After training, AUGUSTUS predicts genes in the input genome file using spliced alignment information from RNA-Seq as extrinsic evidence. Using raw RNAseq data helps to accurately identify exon/intron boundaries better than methods that rely on assembled transcripts.