Schema for LTRharvest - LTR Fragments Identified by LTRharvest
|
|
Database: DvirCAF1 Primary Table: ltrdigest_LTR Row Count: 1,250   Data last updated: 2022-10-20
field | example | SQL type | info |
bin | 585 | smallint(5) unsigned | range |
chrom | scaffold_10054 | varchar(255) | values |
chromStart | 1208 | int(10) unsigned | range |
chromEnd | 5902 | int(10) unsigned | range |
name | LTR_retrotransposon1_LTR | varchar(255) | values |
score | 1000 | int(10) unsigned | range |
strand | + | char(1) | values |
thickStart | 1208 | int(10) unsigned | range |
thickEnd | 5902 | int(10) unsigned | range |
reserved | 0 | int(10) unsigned | range |
blockCount | 2 | int(10) unsigned | range |
blockSizes | 596,595 | longblob | |
chromStarts | 0,4099 | longblob | |
|
| |
|
|
Sample Rows
|
|
bin | chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts |
---|
585 | scaffold_10054 | 1208 | 5902 | LTR_retrotransposon1_LTR | 1000 | + | 1208 | 5902 | 0 | 2 | 596,595 | 0,4099 |
585 | scaffold_10111 | 1125 | 7472 | LTR_retrotransposon2_LTR | 1000 | - | 1125 | 7472 | 0 | 2 | 147,158 | 0,6189 |
585 | scaffold_10127 | 322 | 5784 | LTR_retrotransposon3_LTR | 1000 | + | 322 | 5784 | 0 | 2 | 539,527 | 0,4935 |
585 | scaffold_10156 | 527 | 6932 | LTR_retrotransposon4_LTR | 1000 | - | 527 | 6932 | 0 | 2 | 91,95 | 0,6310 |
585 | scaffold_10240 | 4 | 9566 | LTR_retrotransposon5_LTR | 1000 | + | 4 | 9566 | 0 | 2 | 757,719 | 0,8843 |
585 | scaffold_10257 | 7073 | 15145 | LTR_retrotransposon6_LTR | 1000 | + | 7073 | 15145 | 0 | 2 | 698,723 | 0,7349 |
585 | scaffold_10304 | 69 | 7424 | LTR_retrotransposon7_LTR | 1000 | + | 69 | 7424 | 0 | 2 | 266,254 | 0,7101 |
585 | scaffold_10308 | 1003 | 7802 | LTR_retrotransposon8_LTR | 1000 | + | 1003 | 7802 | 0 | 2 | 111,110 | 0,6689 |
585 | scaffold_10309 | 1354 | 8506 | LTR_retrotransposon9_LTR | 1000 | - | 1354 | 8506 | 0 | 2 | 412,412 | 0,6740 |
585 | scaffold_10322 | 27336 | 33719 | LTR_retrotransposon10_LTR | 1000 | + | 27336 | 33719 | 0 | 2 | 446,425 | 0,5958 |
|
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. virilis 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.
| |
|
|
|