Schema for LTRharvest - LTR Fragments Identified by LTRharvest
|
|
Database: DpseGB3 Primary Table: ltrdigest_LTR Row Count: 414   Data last updated: 2022-10-20
field | example | SQL type | info |
bin | 592 | smallint(5) unsigned | range |
chrom | CH379059 | varchar(255) | values |
chromStart | 966586 | int(10) unsigned | range |
chromEnd | 970716 | int(10) unsigned | range |
name | LTR_retrotransposon1_LTR | varchar(255) | values |
score | 1000 | int(10) unsigned | range |
strand | - | char(1) | values |
thickStart | 966586 | int(10) unsigned | range |
thickEnd | 970716 | int(10) unsigned | range |
reserved | 0 | int(10) unsigned | range |
blockCount | 2 | int(10) unsigned | range |
blockSizes | 766,762 | longblob | |
chromStarts | 0,3368 | longblob | |
|
| |
|
|
Sample Rows
|
|
bin | chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts |
---|
592 | CH379059 | 966586 | 970716 | LTR_retrotransposon1_LTR | 1000 | - | 966586 | 970716 | 0 | 2 | 766,762 | 0,3368 |
592 | CH379059 | 972651 | 976833 | LTR_retrotransposon2_LTR | 1000 | + | 972651 | 976833 | 0 | 2 | 1364,1353 | 0,2829 |
592 | CH379059 | 1011764 | 1017064 | LTR_retrotransposon3_LTR | 1000 | + | 1011764 | 1017064 | 0 | 2 | 186,197 | 0,5103 |
593 | CH379059 | 1080584 | 1085355 | LTR_retrotransposon4_LTR | 1000 | - | 1080584 | 1085355 | 0 | 2 | 651,652 | 0,4119 |
635 | CH379060 | 6604067 | 6616045 | LTR_retrotransposon5_LTR | 1000 | - | 6604067 | 6616045 | 0 | 2 | 1630,1631 | 0,10347 |
639 | CH379060 | 7110475 | 7117215 | LTR_retrotransposon6_LTR | 1000 | - | 7110475 | 7117215 | 0 | 2 | 344,337 | 0,6403 |
623 | CH379061 | 4988108 | 4991058 | LTR_retrotransposon7_LTR | 1000 | + | 4988108 | 4991058 | 0 | 2 | 687,667 | 0,2283 |
590 | CH379063 | 704361 | 711405 | LTR_retrotransposon8_LTR | 1000 | - | 704361 | 711405 | 0 | 2 | 195,200 | 0,6844 |
598 | CH379063 | 1738562 | 1749581 | LTR_retrotransposon9_LTR | 1000 | + | 1738562 | 1749581 | 0 | 2 | 189,188 | 0,10831 |
599 | CH379063 | 1885710 | 1891504 | LTR_retrotransposon10_LTR | 1000 | + | 1885710 | 1891504 | 0 | 2 | 283,267 | 0,5527 |
|
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
-
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.
| |
|
|
|