Schema for LTRharvest - LTR Fragments Identified by LTRharvest
  Database: DanaCAF1    Primary Table: ltrdigest_LTR    Row Count: 2,981   Data last updated: 2022-10-20
fieldexampleSQL type info
bin 585smallint(5) unsigned range
chrom scaffold_10015varchar(255) values
chromStart 1271int(10) unsigned range
chromEnd 7271int(10) unsigned range
name LTR_retrotransposon1_LTRvarchar(255) values
score 1000int(10) unsigned range
strand +char(1) values
thickStart 1271int(10) unsigned range
thickEnd 7271int(10) unsigned range
reserved 0int(10) unsigned range
blockCount 2int(10) unsigned range
blockSizes 271,282longblob  
chromStarts 0,5718longblob  

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStarts
585scaffold_1001512717271LTR_retrotransposon1_LTR1000+1271727102271,2820,5718
585scaffold_1002253127851LTR_retrotransposon2_LTR1000-5312785102274,2700,2269
585scaffold_1002913057100LTR_retrotransposon3_LTR1000+1305710002294,2950,5500
585scaffold_1003922677685LTR_retrotransposon4_LTR1000-2267768502198,2080,5210
585scaffold_100391556819443LTR_retrotransposon5_LTR1000-15568194430297,950,3780
585scaffold_100395570662799LTR_retrotransposon6_LTR1000+557066279902885,8910,6202
585scaffold_100485943109LTR_retrotransposon7_LTR1000-594310902281,2770,2238
585scaffold_10048513512150LTR_retrotransposon8_LTR1000-51351215002346,3480,6667
585scaffold_100484906658016LTR_retrotransposon9_LTR1000+490665801602613,6120,8338
585scaffold_100521145115329LTR_retrotransposon10_LTR1000-114511532902685,6950,3183

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

LTRharvest (ltrdigest) Track Description
 

Description

LTRharvest is used to identify putative long terminal repeats (LTR) retrotransposons in the D. ananassae 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