LTRharvest Track Settings

LTR Fragments Identified by LTRharvest (All Variation and Repeats tracks)

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	hide Configure	LTR Retrotransposons	LTR Retrotransposons Identified by LTRharvest	Schema
	hide Configure	Terminal Repeats	Long Terminal Repeats Identified by LTRharvest	Schema
	hide Configure	TSD Sites	Target Site Duplications Identified by LTRharvest	Schema
	hide Configure	PBS Sites	Primer Binding Sites Identified by LTRharvest	Schema
	hide Configure	TE Proteins	Transposon Proteins Matches Identified by LTRharvest	Schema
	hide Configure	PPT Sites	Polypurine Tract Sites Identified by LTRharvest	Schema

Description

LTRharvest is used to identify putative long terminal repeats (LTR) retrotransposons in the D. mojavensis genome using the following parameters:

Additional features within the LTR retrotransposons are annotated using LTRdigest.

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).