Schema for LTRharvest - LTR Fragments Identified by LTRharvest

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Schema for LTRharvest - LTR Fragments Identified by LTRharvest

Database: DmojImproved Primary Table: ltrharvest_long_terminal_repeat Row Count: 4,067

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	547	`int(10) unsigned`	range
`chromEnd`	15515	`int(10) unsigned`	range
`name`	LTR_retrotransposon1	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	547	`int(10) unsigned`	range
`thickEnd`	15515	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	662,658	`longblob`
`chromStarts`	0,14310	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	reserved	blockCount	blockSizes	chromStarts
585	improved_6498	547	15515	LTR_retrotransposon1	1000	+	547	15515	0	2	662,658	0,14310
585	improved_6498	55758	59761	LTR_retrotransposon2	1000	+	55758	59761	0	2	297,301	0,3702
585	improved_6498	74781	87475	LTR_retrotransposon3	1000	+	74781	87475	0	2	325,332	0,12362
585	improved_6498	88508	99923	LTR_retrotransposon4	1000	+	88508	99923	0	2	295,302	0,11113
585	improved_6498	101068	110690	LTR_retrotransposon5	1000	+	101068	110690	0	2	147,155	0,9467
585	improved_6498	121042	123720	LTR_retrotransposon6	1000	+	121042	123720	0	2	237,237	0,2441
586	improved_6498	138776	144830	LTR_retrotransposon7	1000	+	138776	144830	0	2	197,182	0,5872
586	improved_6498	156890	171308	LTR_retrotransposon8	1000	+	156890	171308	0	2	145,143	0,14275
586	improved_6498	176547	182377	LTR_retrotransposon9	1000	+	176547	182377	0	2	179,177	0,5653
586	improved_6498	186676	191742	LTR_retrotransposon10	1000	+	186676	191742	0	2	387,399	0,4667

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

LTRharvest (ltr_harvest) Track Description


	Description LTRharvest is used to identify putative long terminal repeats (LTR) retrotransposons in the D. mojavensis genome using the following parameters: -mintsd 4 -maxtsd 20 -minlenltr 100 -maxlenltr 1000 -mindistltr 1000 -maxdistltr 15000 Additional features within the LTR retrotransposons are annotated using LTRdigest. References D. Ellinghaus, S. Kurtz, and U. Willhoeft. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics, 9:18, 2008. S. Steinbiss, U. Willhoeft, G. Gremme and S. Kurtz. Fine-grained annotation and classification of de novo predicted LTR retrotransposons. Nucleic Acids Research, 37(21):7002-7013 (2009).