Schema for LTRharvest - LTR Fragments Identified by LTRharvest

Database: DbipGB2 Primary Table: ltrdigest_LTR Row Count: 969 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFE02000046	`varchar(255)`	values
`chromStart`	4782	`int(10) unsigned`	range
`chromEnd`	6839	`int(10) unsigned`	range
`name`	LTR_retrotransposon1_LTR	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	4782	`int(10) unsigned`	range
`thickEnd`	6839	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	91,95	`longblob`
`chromStarts`	0,1962	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AFFE02000046	4782	6839	LTR_retrotransposon1_LTR	1000	+	4782	6839	2	91,95	0,1962
585	AFFE02000175	1517	4450	LTR_retrotransposon2_LTR	1000	+	1517	4450	2	258,250	0,2683
585	AFFE02000193	438	5723	LTR_retrotransposon3_LTR	1000	+	438	5723	2	314,304	0,4981
585	AFFE02000235	3941	12773	LTR_retrotransposon4_LTR	1000	-	3941	12773	2	209,206	0,8626
585	AFFE02000289	202	4885	LTR_retrotransposon5_LTR	1000	-	202	4885	2	209,204	0,4479
585	AFFE02000353	3125	12971	LTR_retrotransposon6_LTR	1000	-	3125	12971	2	265,254	0,9592
585	AFFE02000362	1723	6014	LTR_retrotransposon7_LTR	1000	-	1723	6014	2	119,103	0,4188
585	AFFE02000407	366	12279	LTR_retrotransposon8_LTR	1000	+	366	12279	2	118,121	0,11792
585	AFFE02000444	564	8033	LTR_retrotransposon9_LTR	1000	+	564	8033	2	410,405	0,7064
585	AFFE02000474	2011	7300	LTR_retrotransposon10_LTR	1000	+	2011	7300	2	311,302	0,4987

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. bipectinata 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