Repetitive element annotation protocol for the eastern banjo frog
Qiye Li, Qunfei Guo, Yang Zhou, Huishuang Tan, Terry Bertozzi, Yuanzhen Zhu, Ji Li, Stephen Donnellan, Guojie Zhang
Abstract
This pipeline is the repetitive element annotation by using homology-based, de novo predictions and Tandem Repeats Finder to identify repetitive elements in the Limnodynastes dumerilii dumerilii genome assembly.
Steps
The following sub-steps are the process for homology-based predictions to identify repetitive elements in the Limnodynastes dumerilii dumerilii genome assembly. Limnodynastes dumerilii dumerilii genome assembly.
Identify known repetitive elements by aligning the Limnodynastes dumerilii dumerilii genome sequences against the Repbase-derived RepeatMasker libraries using RepeatMasker (v4.1.0).
Identify known repetitive elements by aligning the Limnodynastes dumerilii dumerilii genome sequences against the transposable element protein database using RepeatProteinMask (an application within the RepeatMasker package)
The following sub-steps are the process for de novo predictions to identify repetitive elements in the Limnodynastes dumerilii dumerilii genome assembly. de novo predictions to identify repetitive elements in the Limnodynastes dumerilii dumerilii genome assembly.
Execute RepeatModeler (v2.0, RRID:SCR_015027) on the Limnodynastes dumerilii dumerilii assembly to build a de novo repeat library for this species.
Employ RepeatMasker (v4.1.0) to align the Limnodynastes dumerilii dumerilii genome sequences against the de novo library for repetitive element identification.
Identify tandem repeats in the Limnodynastes dumerilii dumerilii genome assembly by Tandem Repeats Finder (v4.09). Limnodynastes dumerilii dumerilii genome assembly by Tandem Repeats Finder (v4.09).
