Schema for LTRharvest - LTR Fragments Identified by LTRharvest |
|---|
| |
Database: DobsGB1 Primary Table: ltrdigest_protein Row Count: 12,486 Data last updated: 2022-10-20
| field | example | SQL type | info |
|---|
| bin | 589 | smallint(5) unsigned | range |
| chrom | BDQP01000001 | varchar(255) | values |
| chromStart | 529980 | int(10) unsigned | range |
| chromEnd | 530647 | int(10) unsigned | range |
| name | RVT_1 | varchar(255) | values |
| score | 0 | int(10) unsigned | range |
| strand | - | char(1) | values |
| thickStart | 0 | int(10) unsigned | range |
|
| |
|
|
|
Sample Rows
|
|---|
| |
| bin | chrom | chromStart | chromEnd | name | score | strand | thickStart |
|---|
| 589 | BDQP01000001 | 529980 | 530647 | RVT_1 | 0 | - | 0 |
| 589 | BDQP01000001 | 531570 | 531874 | Exo_endo_phos_2 | 0 | - | 0 |
| 597 | BDQP01000001 | 1617363 | 1617622 | Retrotrans_gag | 0 | + | 0 |
| 597 | BDQP01000001 | 1618250 | 1618536 | RVP | 0 | + | 0 |
| 597 | BDQP01000001 | 1618256 | 1619523 | GAGCOATPOL_caulimoviridae | 0 | + | 0 |
| 597 | BDQP01000001 | 1618268 | 1619523 | MOVCOATPOL_caulimoviridae | 0 | + | 0 |
| 597 | BDQP01000001 | 1618271 | 1618530 | Asp_protease_2 | 0 | + | 0 |
| 597 | BDQP01000001 | 1618292 | 1618440 | gag-asp_proteas | 0 | + | 0 |
| 597 | BDQP01000001 | 1618298 | 1619526 | POL_caulimoviridae_Biology_Direct_4_41_2009 | 0 | + | 0 |
| 597 | BDQP01000001 | 1618301 | 1618539 | AP_clanaa_Biology_Direct_4-3_2009 | 0 | + | 0 |
|
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. obscura 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.
| |
|
|
|