Schema for LTRharvest - LTR Fragments Identified by LTRharvest
|
|
Database: DkikGB2 Primary Table: ltrdigest_LTR Row Count: 713   Data last updated: 2022-10-20
field | example | SQL type | info |
bin | 585 | smallint(5) unsigned | range |
chrom | AFFH02000165 | varchar(255) | values |
chromStart | 6383 | int(10) unsigned | range |
chromEnd | 13091 | int(10) unsigned | range |
name | LTR_retrotransposon1_LTR | varchar(255) | values |
score | 1000 | int(10) unsigned | range |
strand | - | char(1) | values |
thickStart | 6383 | int(10) unsigned | range |
thickEnd | 13091 | int(10) unsigned | range |
reserved | 0 | int(10) unsigned | range |
blockCount | 2 | int(10) unsigned | range |
blockSizes | 467,456 | longblob | |
chromStarts | 0,6252 | longblob | |
|
| |
|
|
Sample Rows
|
|
bin | chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts |
---|
585 | AFFH02000165 | 6383 | 13091 | LTR_retrotransposon1_LTR | 1000 | - | 6383 | 13091 | 0 | 2 | 467,456 | 0,6252 |
585 | AFFH02000165 | 16612 | 19785 | LTR_retrotransposon2_LTR | 1000 | + | 16612 | 19785 | 0 | 2 | 1035,1046 | 0,2127 |
585 | AFFH02000165 | 22789 | 33371 | LTR_retrotransposon3_LTR | 1000 | + | 22789 | 33371 | 0 | 2 | 358,356 | 0,10226 |
585 | AFFH02000402 | 96 | 3074 | LTR_retrotransposon4_LTR | 1000 | - | 96 | 3074 | 0 | 2 | 484,488 | 0,2490 |
585 | AFFH02000405 | 4024 | 5427 | LTR_retrotransposon5_LTR | 1000 | - | 4024 | 5427 | 0 | 2 | 286,275 | 0,1128 |
585 | AFFH02000554 | 12426 | 16226 | LTR_retrotransposon6_LTR | 1000 | - | 12426 | 16226 | 0 | 2 | 1147,1146 | 0,2654 |
585 | AFFH02000593 | 5974 | 11911 | LTR_retrotransposon7_LTR | 1000 | + | 5974 | 11911 | 0 | 2 | 253,252 | 0,5685 |
585 | AFFH02000602 | 1374 | 8758 | LTR_retrotransposon8_LTR | 1000 | + | 1374 | 8758 | 0 | 2 | 353,355 | 0,7029 |
585 | AFFH02000679 | 2104 | 14013 | LTR_retrotransposon9_LTR | 1000 | - | 2104 | 14013 | 0 | 2 | 1634,1641 | 0,10268 |
585 | AFFH02000832 | 2077 | 7490 | LTR_retrotransposon10_LTR | 1000 | + | 2077 | 7490 | 0 | 2 | 201,213 | 0,5200 |
|
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. kikkawai 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.
| |
|
|
|