Schema for LTRharvest - LTR Fragments Identified by LTRharvest

Database: DperCAF1 Primary Table: ltrdigest_LTR Row Count: 1,353 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	644	`smallint(5) unsigned`	range
`chrom`	super_0	`varchar(255)`	values
`chromStart`	7827030	`int(10) unsigned`	range
`chromEnd`	7829513	`int(10) unsigned`	range
`name`	LTR_retrotransposon1_LTR	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	7827030	`int(10) unsigned`	range
`thickEnd`	7829513	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	788,776	`longblob`
`chromStarts`	0,1707	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
644	super_0	7827030	7829513	LTR_retrotransposon1_LTR	1000	+	7827030	7829513	2	788,776	0,1707
674	super_0	11751212	11759047	LTR_retrotransposon2_LTR	1000	-	11751212	11759047	2	533,520	0,7315
674	super_0	11766793	11772027	LTR_retrotransposon3_LTR	1000	-	11766793	11772027	2	249,250	0,4984
84	super_0	11790151	11797910	LTR_retrotransposon4_LTR	1000	-	11790151	11797910	2	544,533	0,7226
586	super_10	172277	179306	LTR_retrotransposon5_LTR	1000	+	172277	179306	2	491,486	0,6543
586	super_10	193214	195381	LTR_retrotransposon6_LTR	1000	+	193214	195381	2	123,128	0,2039
607	super_10	2971499	2977941	LTR_retrotransposon7_LTR	1000	+	2971499	2977941	2	475,475	0,5967
585	super_100	39641	46127	LTR_retrotransposon8_LTR	1000	+	39641	46127	2	1402,1400	0,5086
585	super_100	77316	89048	LTR_retrotransposon9_LTR	1000	+	77316	89048	2	1976,1999	0,9733
585	super_100	105002	111459	LTR_retrotransposon10_LTR	1000	+	105002	111459	2	166,157	0,6300

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. persimilis 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

References