Schema for LTRharvest - LTR Fragments Identified by LTRharvest

Database: DmirGB2 Primary Table: ltrdigest_LTR Row Count: 171 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	591	`smallint(5) unsigned`	range
`chrom`	CM001516	`varchar(255)`	values
`chromStart`	799661	`int(10) unsigned`	range
`chromEnd`	811467	`int(10) unsigned`	range
`name`	LTR_retrotransposon1_LTR	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	799661	`int(10) unsigned`	range
`thickEnd`	811467	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	342,343	`longblob`
`chromStarts`	0,11463	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
591	CM001516	799661	811467	LTR_retrotransposon1_LTR	1000	-	799661	811467	2	342,343	0,11463
591	CM001516	818052	823301	LTR_retrotransposon2_LTR	1000	-	818052	823301	2	173,174	0,5075
592	CM001516	938317	944551	LTR_retrotransposon3_LTR	1000	+	938317	944551	2	100,96	0,6138
592	CM001516	1027583	1033872	LTR_retrotransposon4_LTR	1000	-	1027583	1033872	2	272,276	0,6013
593	CM001516	1143635	1152251	LTR_retrotransposon5_LTR	1000	+	1143635	1152251	2	266,268	0,8348
596	CM001516	1559483	1566075	LTR_retrotransposon6_LTR	1000	+	1559483	1566075	2	156,154	0,6438
597	CM001516	1576838	1581077	LTR_retrotransposon7_LTR	1000	+	1576838	1581077	2	294,290	0,3949
597	CM001516	1584254	1595723	LTR_retrotransposon8_LTR	1000	+	1584254	1595723	2	189,199	0,11270
601	CM001516	2174690	2180261	LTR_retrotransposon9_LTR	1000	+	2174690	2180261	2	283,284	0,5287
601	CM001516	2204242	2209003	LTR_retrotransposon10_LTR	1000	-	2204242	2209003	2	311,312	0,4449

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.

Description

References