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

Display mode:       Reset to defaults

Show only items with score at or above:   (range: 0 to 1000)

List subtracks: only selected/visible    all    ()  
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. yakuba 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