Schema for LTRharvest - LTR Fragments Identified by LTRharvest

Database: DbiaGB2 Primary Table: ltrdigest_LTR Row Count: 1,082 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFD02000073	`varchar(255)`	values
`chromStart`	9330	`int(10) unsigned`	range
`chromEnd`	16670	`int(10) unsigned`	range
`name`	LTR_retrotransposon1_LTR	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	9330	`int(10) unsigned`	range
`thickEnd`	16670	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	180,184	`longblob`
`chromStarts`	0,7156	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AFFD02000073	9330	16670	LTR_retrotransposon1_LTR	1000	-	9330	16670	2	180,184	0,7156
585	AFFD02000085	9	10804	LTR_retrotransposon2_LTR	1000	+	9	10804	2	1143,1141	0,9654
585	AFFD02000090	5	7229	LTR_retrotransposon3_LTR	1000	-	5	7229	2	1993,1985	0,5239
585	AFFD02000180	1809	6324	LTR_retrotransposon4_LTR	1000	-	1809	6324	2	1227,1218	0,3297
585	AFFD02000186	58407	66960	LTR_retrotransposon5_LTR	1000	+	58407	66960	2	219,215	0,8338
585	AFFD02000186	73203	79209	LTR_retrotransposon6_LTR	1000	+	73203	79209	2	349,340	0,5666
585	AFFD02000233	11355	19249	LTR_retrotransposon7_LTR	1000	-	11355	19249	2	80,92	0,7802
585	AFFD02000233	25177	29817	LTR_retrotransposon8_LTR	1000	-	25177	29817	2	513,483	0,4157
585	AFFD02000293	22724	26997	LTR_retrotransposon9_LTR	1000	-	22724	26997	2	83,90	0,4183
585	AFFD02000310	1967	7241	LTR_retrotransposon10_LTR	1000	+	1967	7241	2	302,296	0,4978

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. biarmipes 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