Combined Evidence Annotation of Transposable Elements in Genome Sequences
Figure 1
Schematic of Our TE Annotation Pipeline
The pipeline is composed of (i) known TE family detection methods such as BLRn, RM, and RMBLR; (ii) satellite detection software such as RM, TRF, and Mreps; (iii) anonymous TE detection methods such BLRa, TE-HMM, RECON, and BLRtx; and (iv) a MySQL database called REPET to manage the results and the annotations. GAME-XML files are then generated from the results stored in the database and loaded into the Apollo genome annotation tool, allowing automatic results to be manually curated to produce a reliable annotation. To facilitate manual curation, we automatically promoted RMBLR results to be the candidate annotation.