Schema for LTRharvest - LTR Fragments Identified by LTRharvest
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Database: DyakCAF1 Primary Table: ltrdigest_TSD Row Count: 1,305   Data last updated: 2022-10-20
field | example | SQL type | info |
bin | 593 | smallint(5) unsigned | range |
chrom | chr2L | varchar(255) | values |
chromStart | 1156888 | int(10) unsigned | range |
chromEnd | 1162133 | int(10) unsigned | range |
name | repeat_region1_TSD | varchar(255) | values |
score | 1000 | int(10) unsigned | range |
strand | + | char(1) | values |
thickStart | 1156888 | int(10) unsigned | range |
thickEnd | 1162133 | int(10) unsigned | range |
reserved | 0 | int(10) unsigned | range |
blockCount | 2 | int(10) unsigned | range |
blockSizes | 4,4 | longblob | |
chromStarts | 0,5241 | longblob | |
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Sample Rows
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bin | chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts |
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593 | chr2L | 1156888 | 1162133 | repeat_region1_TSD | 1000 | + | 1156888 | 1162133 | 0 | 2 | 4,4 | 0,5241 |
636 | chr2L | 6758430 | 6759966 | repeat_region2_TSD | 1000 | + | 6758430 | 6759966 | 0 | 2 | 4,4 | 0,1532 |
696 | chr2L | 14573225 | 14576909 | repeat_region3_TSD | 1000 | - | 14573225 | 14576909 | 0 | 2 | 4,4 | 0,3680 |
699 | chr2L | 15014750 | 15021481 | repeat_region4_TSD | 1000 | + | 15014750 | 15021481 | 0 | 2 | 4,4 | 0,6727 |
710 | chr2L | 16421601 | 16425136 | repeat_region5_TSD | 1000 | - | 16421601 | 16425136 | 0 | 2 | 4,4 | 0,3531 |
730 | chr2L | 19051931 | 19056167 | repeat_region6_TSD | 1000 | - | 19051931 | 19056167 | 0 | 2 | 4,4 | 0,4232 |
735 | chr2L | 19699860 | 19704959 | repeat_region7_TSD | 1000 | + | 19699860 | 19704959 | 0 | 2 | 4,4 | 0,5095 |
741 | chr2L | 20556610 | 20561349 | repeat_region8_TSD | 1000 | + | 20556610 | 20561349 | 0 | 2 | 4,4 | 0,4735 |
742 | chr2L | 20690452 | 20702975 | repeat_region9_TSD | 1000 | - | 20690452 | 20702975 | 0 | 2 | 4,4 | 0,12519 |
745 | chr2L | 21014893 | 21020970 | repeat_region10_TSD | 1000 | + | 21014893 | 21020970 | 0 | 2 | 4,4 | 0,6073 |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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LTRharvest (ltrdigest) Track Description
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Description
LTRharvest
is used to identify putative long terminal repeats (LTR)
retrotransposons in the D. yakuba 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
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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.
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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).
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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.
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