Schema for LTRharvest - LTR Fragments Identified by LTRharvest

Database: DserGB1 Primary Table: ltrdigest_LTR Row Count: 1,048 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	MTTC01000008	`varchar(255)`	values
`chromStart`	663	`int(10) unsigned`	range
`chromEnd`	9271	`int(10) unsigned`	range
`name`	LTR_retrotransposon1_LTR	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	663	`int(10) unsigned`	range
`thickEnd`	9271	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	566,573	`longblob`
`chromStarts`	0,8035	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	MTTC01000008	663	9271	LTR_retrotransposon1_LTR	1000	+	663	9271	2	566,573	0,8035
585	MTTC01000009	38921	53199	LTR_retrotransposon2_LTR	1000	+	38921	53199	2	139,136	0,14142
585	MTTC01000009	57252	62093	LTR_retrotransposon3_LTR	1000	-	57252	62093	2	217,203	0,4638
585	MTTC01000009	65953	71963	LTR_retrotransposon4_LTR	1000	-	65953	71963	2	322,321	0,5689
585	MTTC01000009	76994	89521	LTR_retrotransposon5_LTR	1000	+	76994	89521	2	195,184	0,12343
586	MTTC01000009	146139	149237	LTR_retrotransposon6_LTR	1000	+	146139	149237	2	200,193	0,2905
586	MTTC01000009	184993	195425	LTR_retrotransposon7_LTR	1000	-	184993	195425	2	1997,1995	0,8437
586	MTTC01000009	243805	255574	LTR_retrotransposon8_LTR	1000	-	243805	255574	2	308,318	0,11451
587	MTTC01000009	323622	326614	LTR_retrotransposon9_LTR	1000	+	323622	326614	2	246,256	0,2736
587	MTTC01000009	328758	335689	LTR_retrotransposon10_LTR	1000	-	328758	335689	2	538,528	0,6403

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. serrata 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