2.4 | Annotation of repetitive sequences
Both homology-based and de novo- based approaches were used
to search for TEs. Tandem Repeat was extracted using TRF
(http://tandem.bu.edu/trf/trf.html) by ab initio prediction. The
homolog prediction used Repbase (http://www.girinst.org /repbase)
database employing RepeatMasker
(http://www.repeatmasker.org/)
software and its in-house scripts (RepeatProteinMask) with default
parameters to extract repeat regions. For the de novo-based approach, we
used LTR_FINDER
(http://tlife.fudan.edu.cn/ltr_finder/),
RepeatScout
(http://www.repeatmasker.org/),
and RepeatModeler (http://www.repeatmasker.org/RepeatModeler.html) to
build the de novo repeat library. All the repeats identified by
different methods were combined into the final repeat annotation after
removing the redundant repeats.