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. pseudoobscura 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.