Schema for LTRharvest - LTR Fragments Identified by LTRharvest

Database: DrhoGB2 Primary Table: ltrdigest_retrotransposon Row Count: 1,193 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFPP02003242	`varchar(255)`	values
`chromStart`	406	`int(10) unsigned`	range
`chromEnd`	2770	`int(10) unsigned`	range
`name`	LTR_retrotransposon1	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand
585	AFPP02003242	406	2770	LTR_retrotransposon1	1000	+
585	AFPP02003256	3464	9859	LTR_retrotransposon2	1000	+
585	AFPP02003448	8	2821	LTR_retrotransposon3	1000	+
585	AFPP02003555	14415	18605	LTR_retrotransposon4	1000	-
585	AFPP02003585	9749	15109	LTR_retrotransposon5	1000	+
585	AFPP02003680	2906	10604	LTR_retrotransposon6	1000	-
585	AFPP02003745	10851	13692	LTR_retrotransposon7	1000	+
585	AFPP02003895	1027	3490	LTR_retrotransposon8	1000	+
585	AFPP02004020	279	1490	LTR_retrotransposon9	1000	-
585	AFPP02004355	2977	9337	LTR_retrotransposon10	1000	-

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. rhopaloa 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