Schema for LTRharvest - LTR Fragments Identified by LTRharvest
  Database: DpseGB3    Primary Table: ltrdigest_LTR    Row Count: 414   Data last updated: 2022-10-20
fieldexampleSQL type info
bin 592smallint(5) unsigned range
chrom CH379059varchar(255) values
chromStart 966586int(10) unsigned range
chromEnd 970716int(10) unsigned range
name LTR_retrotransposon1_LTRvarchar(255) values
score 1000int(10) unsigned range
strand -char(1) values
thickStart 966586int(10) unsigned range
thickEnd 970716int(10) unsigned range
reserved 0int(10) unsigned range
blockCount 2int(10) unsigned range
blockSizes 766,762longblob  
chromStarts 0,3368longblob  

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStarts
592CH379059966586970716LTR_retrotransposon1_LTR1000-96658697071602766,7620,3368
592CH379059972651976833LTR_retrotransposon2_LTR1000+972651976833021364,13530,2829
592CH37905910117641017064LTR_retrotransposon3_LTR1000+1011764101706402186,1970,5103
593CH37905910805841085355LTR_retrotransposon4_LTR1000-1080584108535502651,6520,4119
635CH37906066040676616045LTR_retrotransposon5_LTR1000-66040676616045021630,16310,10347
639CH37906071104757117215LTR_retrotransposon6_LTR1000-7110475711721502344,3370,6403
623CH37906149881084991058LTR_retrotransposon7_LTR1000+4988108499105802687,6670,2283
590CH379063704361711405LTR_retrotransposon8_LTR1000-70436171140502195,2000,6844
598CH37906317385621749581LTR_retrotransposon9_LTR1000+1738562174958102189,1880,10831
599CH37906318857101891504LTR_retrotransposon10_LTR1000+1885710189150402283,2670,5527

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. 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