LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo

BMC Genomics

Table 1 Length statistics to determine the default parameters of LtrDetector

		A. thaliana	O. Sativa	G.max	S. bicolor	Z. mays	H. vulgare
LTR length	Maximum	2033	5832	2886	5645	6119	5609
	Minimum	103	109	105	100	97	154
	Mean	495	1128	421	731	679	1840
	Standard deviation	436	1399	356	942	936	1674
Total length	Maximum	14069	20595	18868	22029	20354	16260
	Minimum	824	402	2565	764	536	5143
	Mean	5635	5982	5516	6697	6331	9449
	Standard deviation	2083	2995	1998	2979	2692	3274

These statistics were calculated on LTR-RTs of six plant genomes found in Repbase. In Repbase, an LTR-RT is reported as two sequences: the LTR sequence and the interior sequence. Default length parameters were chosen to approximate the most extreme values found in the dataset, which appear in boldface. To calculate the total length of an LTR-RT, we concatenated two LTR sequences to the two sides of its interior sequence

ISSN: 1471-2164