Schema for LTRharvest - LTR Fragments Identified by LTRharvest

Database: DgriCAF1 Primary Table: ltrdigest_LTR Row Count: 359 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_10014	`varchar(255)`	values
`chromStart`	108	`int(10) unsigned`	range
`chromEnd`	4879	`int(10) unsigned`	range
`name`	LTR_retrotransposon1_LTR	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	108	`int(10) unsigned`	range
`thickEnd`	4879	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	1263,1269	`longblob`
`chromStarts`	0,3502	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	scaffold_10014	108	4879	LTR_retrotransposon1_LTR	1000	+	108	4879	2	1263,1269	0,3502
585	scaffold_10030	10839	19978	LTR_retrotransposon2_LTR	1000	-	10839	19978	2	620,636	0,8503
585	scaffold_10109	4701	9213	LTR_retrotransposon3_LTR	1000	-	4701	9213	2	585,595	0,3917
585	scaffold_10363	1582	10431	LTR_retrotransposon4_LTR	1000	-	1582	10431	2	185,185	0,8664
585	scaffold_105	13	4108	LTR_retrotransposon5_LTR	1000	+	13	4108	2	773,782	0,3313
585	scaffold_10952	606	1871	LTR_retrotransposon6_LTR	1000	+	606	1871	2	239,245	0,1020
585	scaffold_11392	2806	8425	LTR_retrotransposon7_LTR	1000	-	2806	8425	2	115,122	0,5497
585	scaffold_11723	11	10704	LTR_retrotransposon8_LTR	1000	-	11	10704	2	1982,1985	0,8708
585	scaffold_1205	92	3263	LTR_retrotransposon9_LTR	1000	+	92	3263	2	659,658	0,2513
585	scaffold_12333	64	6043	LTR_retrotransposon10_LTR	1000	+	64	6043	2	1223,1230	0,4749

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. grimshawi 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