Schema for LTRharvest - LTR Fragments Identified by LTRharvest

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Schema for LTRharvest - LTR Fragments Identified by LTRharvest

Database: DmirGB2 Primary Table: ltrdigest_PBS Row Count: 8 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	592	`smallint(5) unsigned`	range
`chrom`	CM001516	`varchar(255)`	values
`chromStart`	938417	`int(10) unsigned`	range
`chromEnd`	938435	`int(10) unsigned`	range
`name`	LTR_retrotransposon3_PBS	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand
592	CM001516	938417	938435	LTR_retrotransposon3_PBS	1000	+
609	CM001517	3212101	3212112	LTR_retrotransposon46_PBS	1000	+
595	CM001518	1410703	1410721	LTR_retrotransposon61_PBS	1000	+
685	CM001518	13168666	13168679	LTR_retrotransposon83_PBS	1000	-
700	CM001518	15199441	15199452	LTR_retrotransposon99_PBS	1000	+
591	CM001519	837063	837074	LTR_retrotransposon118_PBS	1000	+
592	CM001519	1001598	1001609	LTR_retrotransposon119_PBS	1000	+
741	CM001520	20530820	20530837	LTR_retrotransposon150_PBS	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. miranda 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.