Schema for LTRharvest - LTR Fragments Identified by LTRharvest

Database: DtakGB2 Primary Table: ltrdigest_TSD Row Count: 785 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFI02000011	`varchar(255)`	values
`chromStart`	115	`int(10) unsigned`	range
`chromEnd`	6975	`int(10) unsigned`	range
`name`	repeat_region1_TSD	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	115	`int(10) unsigned`	range
`thickEnd`	6975	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	4,4	`longblob`
`chromStarts`	0,6856	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AFFI02000011	115	6975	repeat_region1_TSD	1000	-	115	6975	2	4,4	0,6856
585	AFFI02000019	439	2922	repeat_region2_TSD	1000	+	439	2922	2	4,4	0,2479
585	AFFI02000094	4151	8988	repeat_region3_TSD	1000	+	4151	8988	2	4,4	0,4833
585	AFFI02000173	20089	28656	repeat_region4_TSD	1000	+	20089	28656	2	4,4	0,8563
585	AFFI02000228	10309	14764	repeat_region5_TSD	1000	-	10309	14764	2	4,4	0,4451
585	AFFI02000244	4267	7918	repeat_region6_TSD	1000	+	4267	7918	2	4,4	0,3647
585	AFFI02000303	4223	7325	repeat_region7_TSD	1000	+	4223	7325	2	4,4	0,3098
585	AFFI02000317	453	7060	repeat_region8_TSD	1000	-	453	7060	2	4,4	0,6603
585	AFFI02000319	3068	9458	repeat_region9_TSD	1000	+	3068	9458	2	4,4	0,6386
585	AFFI02000504	378	8836	repeat_region10_TSD	1000	+	378	8836	2	4,4	0,8454

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. takahashii 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