Schema for LTRharvest - LTR Fragments Identified by LTRharvest

Database: DereCAF1 Primary Table: ltrdigest_LTR Row Count: 912 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_1308	`varchar(255)`	values
`chromStart`	664	`int(10) unsigned`	range
`chromEnd`	7401	`int(10) unsigned`	range
`name`	LTR_retrotransposon1_LTR	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	664	`int(10) unsigned`	range
`thickEnd`	7401	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	126,128	`longblob`
`chromStarts`	0,6609	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	scaffold_1308	664	7401	LTR_retrotransposon1_LTR	1000	-	664	7401	2	126,128	0,6609
585	scaffold_1340	822	3523	LTR_retrotransposon2_LTR	1000	+	822	3523	2	292,291	0,2410
585	scaffold_1352	2391	4544	LTR_retrotransposon3_LTR	1000	-	2391	4544	2	294,307	0,1846
585	scaffold_1358	2286	5689	LTR_retrotransposon4_LTR	1000	+	2286	5689	2	151,157	0,3246
585	scaffold_1359	200	4163	LTR_retrotransposon5_LTR	1000	-	200	4163	2	609,618	0,3345
585	scaffold_1361	34	7260	LTR_retrotransposon6_LTR	1000	-	34	7260	2	695,725	0,6501
585	scaffold_1368	6262	10112	LTR_retrotransposon7_LTR	1000	+	6262	10112	2	143,139	0,3711
585	scaffold_1369	9	6656	LTR_retrotransposon8_LTR	1000	+	9	6656	2	1990,2000	0,4647
585	scaffold_1374	4967	11825	LTR_retrotransposon9_LTR	1000	-	4967	11825	2	447,448	0,6410
585	scaffold_1378	1368	10622	LTR_retrotransposon10_LTR	1000	+	1368	10622	2	291,285	0,8969

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

LTRharvest (ltrdigest) Track Description


	Description LTRharvest is used to identify putative long terminal repeats (LTR) retrotransposons in the D. erecta genome using the following parameters: `-seed 76 -minlenltr 116 -maxlenltr 800 -mindistltr 2280 -maxdistltr 8773 -similar 91 -xdrop 7 -mat 2 -mis -2 -ins -3 -del -3 -mintsd 4 -maxtsd 20 -vic 60 -overlaps best` Additional features within the LTR retrotransposons are annotated by LTRdigest with the following parameters: `-pptradius 30 -pptlen 8 30 -pptrprob 0.97 -uboxlen 3 30 -pptuprob 0.91 -pbsradius 30 -pbsalilen 11 30 -pbsoffset 0 5 -pbstrnaoffset 0 40 -pbsmaxedist 1 -pbsmatchscore 5 -pbsmismatchscore -10 -pbsinsertionscore -20 -pbsdeletionscore -20 -pdomevalcutoff 1e-6 -maxgaplen 50` The subset of candidates that show significant similarity to Pfam protein domains within LTR retrotransposons are selected and then clustered using the ltrclustering program with the following parameters: `-psmall 80 -plarge 30` References Ellinghaus D, Kurtz S, and Willhoeft U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics, 9:18, 2008. Steinbiss S, Willhoeft U, Gremme G, and Kurtz S. Fine-grained annotation and classification of de novo predicted LTR retrotransposons. Nucleic Acids Research, 37(21):7002-7013 (2009). Steinbiss S, Kastens S, and Kurtz S. LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons. Mob DNA. 2012 Nov 7;3(1):18.

Description