Schema for LTRharvest - LTR Fragments Identified by LTRharvest

Database: DvirCAF1 Primary Table: ltrdigest_TSD Row Count: 1,250 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_10054	`varchar(255)`	values
`chromStart`	1204	`int(10) unsigned`	range
`chromEnd`	5906	`int(10) unsigned`	range
`name`	repeat_region1_TSD	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	1204	`int(10) unsigned`	range
`thickEnd`	5906	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	4,4	`longblob`
`chromStarts`	0,4698	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	scaffold_10054	1204	5906	repeat_region1_TSD	1000	+	1204	5906	2	4,4	0,4698
585	scaffold_10111	1121	7476	repeat_region2_TSD	1000	-	1121	7476	2	4,4	0,6351
585	scaffold_10127	318	5788	repeat_region3_TSD	1000	+	318	5788	2	4,4	0,5466
585	scaffold_10156	523	6936	repeat_region4_TSD	1000	-	523	6936	2	4,4	0,6409
585	scaffold_10240	0	9570	repeat_region5_TSD	1000	+	0	9570	2	4,4	0,9566
585	scaffold_10257	7069	15149	repeat_region6_TSD	1000	+	7069	15149	2	4,4	0,8076
585	scaffold_10304	65	7428	repeat_region7_TSD	1000	+	65	7428	2	4,4	0,7359
585	scaffold_10308	999	7806	repeat_region8_TSD	1000	+	999	7806	2	4,4	0,6803
585	scaffold_10309	1350	8510	repeat_region9_TSD	1000	-	1350	8510	2	4,4	0,7156
585	scaffold_10322	27332	33723	repeat_region10_TSD	1000	+	27332	33723	2	4,4	0,6387

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. virilis 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