2.4 Repetitive sequence annotation
We annotated the repetitive sequences in the P. leopardus genome
with both homology searching in known repeat database and de novopredictions. Known repeats were identified using RepeatMasker (v3.3.0)
(Taraio-Graovac & Chen, 2009) with the RepBase TE library (v14.06) (Bao
et al., 2015). RepeatProteinMask (v3.2.2) implemented in RepeatMasker
was used to detect the TE-relevant proteins. Novel repeats were
predicted using RepeatModeler (http://www.repeatmasker.org) based on thede novo repeat library constructed with LTR_Finder (Xu & Wang,
2007) and RepeatScout (Price et al., 2005). In addition, we used Tandem
Repeat Finder (TRF, v4.09) (Benson, 1999) to identify the tandem repeats
in the genome with parameters of “Match=2, Mismatch=7, Delta=7, PM=80,
PI=10, Minscore=50, and MaxPerid=2000”.