Schema for LTRharvest - LTR Fragments Identified by LTRharvest
|
|
Database: DtakGB2 Primary Table: ltrdigest_retrotransposon Row Count: 785   Data last updated: 2022-10-20
field | example | SQL type | info |
bin | 585 | smallint(5) unsigned | range |
chrom | AFFI02000011 | varchar(255) | values |
chromStart | 119 | int(10) unsigned | range |
chromEnd | 6971 | int(10) unsigned | range |
name | LTR_retrotransposon1 | varchar(255) | values |
score | 1000 | int(10) unsigned | range |
strand | - | char(1) | values |
|
| |
|
|
Sample Rows
|
|
bin | chrom | chromStart | chromEnd | name | score | strand |
---|
585 | AFFI02000011 | 119 | 6971 | LTR_retrotransposon1 | 1000 | - |
585 | AFFI02000019 | 443 | 2918 | LTR_retrotransposon2 | 1000 | + |
585 | AFFI02000094 | 4155 | 8984 | LTR_retrotransposon3 | 1000 | + |
585 | AFFI02000173 | 20093 | 28652 | LTR_retrotransposon4 | 1000 | + |
585 | AFFI02000228 | 10313 | 14760 | LTR_retrotransposon5 | 1000 | - |
585 | AFFI02000244 | 4271 | 7914 | LTR_retrotransposon6 | 1000 | + |
585 | AFFI02000303 | 4227 | 7321 | LTR_retrotransposon7 | 1000 | + |
585 | AFFI02000317 | 457 | 7056 | LTR_retrotransposon8 | 1000 | - |
585 | AFFI02000319 | 3072 | 9454 | LTR_retrotransposon9 | 1000 | + |
585 | AFFI02000504 | 382 | 8832 | LTR_retrotransposon10 | 1000 | + |
|
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. takahashii 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.
| |
|
|
|