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

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