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_primer_binding_site Row Count: 1,145

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	87127	`int(10) unsigned`	range
`chromEnd`	87138	`int(10) unsigned`	range
`name`	LTR_retrotransposon3	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	-	`char(1)`	values

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand
585	improved_6498	87127	87138	LTR_retrotransposon3	1000	-
585	improved_6498	110526	110537	LTR_retrotransposon5	1000	-
585	improved_6498	121281	121296	LTR_retrotransposon6	1000	+
586	improved_6498	144641	144652	LTR_retrotransposon7	1000	-
586	improved_6498	220458	220472	LTR_retrotransposon14	1000	+
586	improved_6498	236115	236126	LTR_retrotransposon15	1000	-
587	improved_6498	263193	263208	LTR_retrotransposon17	1000	-
587	improved_6498	270639	270654	LTR_retrotransposon18	1000	-
587	improved_6498	303892	303903	LTR_retrotransposon22	1000	-
587	improved_6498	306508	306523	LTR_retrotransposon23	1000	+

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).