Schema for LTRharvest - LTR Fragments Identified by LTRharvest
|
|
Database: DmojCAF1 Primary Table: ltrdigest_LTR Row Count: 764   Data last updated: 2022-10-20
field | example | SQL type | info |
bin | 585 | smallint(5) unsigned | range |
chrom | scaffold_134 | varchar(255) | values |
chromStart | 992 | int(10) unsigned | range |
chromEnd | 4977 | int(10) unsigned | range |
name | LTR_retrotransposon1_LTR | varchar(255) | values |
score | 1000 | int(10) unsigned | range |
strand | + | char(1) | values |
thickStart | 992 | int(10) unsigned | range |
thickEnd | 4977 | int(10) unsigned | range |
reserved | 0 | int(10) unsigned | range |
blockCount | 2 | int(10) unsigned | range |
blockSizes | 391,392 | longblob | |
chromStarts | 0,3593 | longblob | |
|
| |
|
|
Sample Rows
|
|
bin | chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts |
---|
585 | scaffold_134 | 992 | 4977 | LTR_retrotransposon1_LTR | 1000 | + | 992 | 4977 | 0 | 2 | 391,392 | 0,3593 |
585 | scaffold_161 | 586 | 3303 | LTR_retrotransposon2_LTR | 1000 | + | 586 | 3303 | 0 | 2 | 234,226 | 0,2491 |
585 | scaffold_1617 | 391 | 6411 | LTR_retrotransposon3_LTR | 1000 | + | 391 | 6411 | 0 | 2 | 138,124 | 0,5896 |
585 | scaffold_1629 | 1449 | 5830 | LTR_retrotransposon4_LTR | 1000 | - | 1449 | 5830 | 0 | 2 | 82,83 | 0,4298 |
585 | scaffold_1639 | 35 | 3736 | LTR_retrotransposon5_LTR | 1000 | - | 35 | 3736 | 0 | 2 | 184,182 | 0,3519 |
585 | scaffold_164 | 904 | 3456 | LTR_retrotransposon6_LTR | 1000 | - | 904 | 3456 | 0 | 2 | 792,800 | 0,1752 |
585 | scaffold_1667 | 2435 | 5128 | LTR_retrotransposon7_LTR | 1000 | - | 2435 | 5128 | 0 | 2 | 276,289 | 0,2404 |
585 | scaffold_1676 | 526 | 7472 | LTR_retrotransposon8_LTR | 1000 | + | 526 | 7472 | 0 | 2 | 649,637 | 0,6309 |
585 | scaffold_1683 | 431 | 5219 | LTR_retrotransposon9_LTR | 1000 | + | 431 | 5219 | 0 | 2 | 829,808 | 0,3980 |
585 | scaffold_1696 | 14 | 3175 | LTR_retrotransposon10_LTR | 1000 | - | 14 | 3175 | 0 | 2 | 632,640 | 0,2521 |
|
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. mojavensis 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.
| |
|
|
|