Schema for LTRharvest - LTR Fragments Identified by LTRharvest

Database: DeugGB2 Primary Table: ltrdigest_LTR Row Count: 1,186 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFPQ02000031	`varchar(255)`	values
`chromStart`	26274	`int(10) unsigned`	range
`chromEnd`	31275	`int(10) unsigned`	range
`name`	LTR_retrotransposon1_LTR	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	26274	`int(10) unsigned`	range
`thickEnd`	31275	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	255,265	`longblob`
`chromStarts`	0,4736	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AFPQ02000031	26274	31275	LTR_retrotransposon1_LTR	1000	+	26274	31275	2	255,265	0,4736
585	AFPQ02000031	35050	40718	LTR_retrotransposon2_LTR	1000	-	35050	40718	2	172,172	0,5496
585	AFPQ02000176	8305	18619	LTR_retrotransposon3_LTR	1000	+	8305	18619	2	249,250	0,10064
585	AFPQ02000204	834	5452	LTR_retrotransposon4_LTR	1000	-	834	5452	2	1440,1425	0,3193
585	AFPQ02000231	4496	5690	LTR_retrotransposon5_LTR	1000	-	4496	5690	2	99,98	0,1096
585	AFPQ02000231	21705	24882	LTR_retrotransposon6_LTR	1000	-	21705	24882	2	424,432	0,2745
585	AFPQ02000290	355	8026	LTR_retrotransposon7_LTR	1000	+	355	8026	2	1318,1332	0,6339
585	AFPQ02000290	18064	24976	LTR_retrotransposon8_LTR	1000	+	18064	24976	2	335,315	0,6597
585	AFPQ02000294	8017	12403	LTR_retrotransposon9_LTR	1000	-	8017	12403	2	324,324	0,4062
585	AFPQ02000303	5352	9748	LTR_retrotransposon10_LTR	1000	+	5352	9748	2	319,317	0,4079

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. eugracilis 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