Organization and evolution of transposable elements along the bread wheat chromosome 3B

Table 1 Comparison of the accuracy of transposable element modeling on a 1 Mb scaffold of wheat chromosome 3B

		Reference	RM	TEannot	CLARI-TE
Number of predictions		196	590	345	286
Coverage		91%	90%	90%	91%
Nucleotide	Sn	-	93%	95%	96%
Nucleotide	Sp	-	96%	97%	95%
Feature	Sn	-	54%	45%	66%
Feature	Sp	-	26%	27%	52%
Nested feature	Sn	-	NA	17%	41%
Nested feature	Sp	-	NA	14%	58%

The reference annotation was curated manually. Similarity search was performed using RepeatMasker (RM) and automated TE modeling based on the RM results was performed using either TEannot or CLARI-TE. The sensitivity (Sn) and specificity (Sp) were calculated at three different levels: nucleotide, feature and nested feature (see Materials and methods). NA, not applicable.

ISSN: 1474-760X