Schema for LTRharvest - LTR Fragments Identified by LTRharvest
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Database: DsuzGB1 Primary Table: ltrdigest_TSD Row Count: 1,854   Data last updated: 2022-10-20
field | example | SQL type | info |
bin | 585 | smallint(5) unsigned | range |
chrom | AWUT01012676 | varchar(255) | values |
chromStart | 5593 | int(10) unsigned | range |
chromEnd | 16794 | int(10) unsigned | range |
name | repeat_region1_TSD | varchar(255) | values |
score | 1000 | int(10) unsigned | range |
strand | + | char(1) | values |
thickStart | 5593 | int(10) unsigned | range |
thickEnd | 16794 | int(10) unsigned | range |
reserved | 0 | int(10) unsigned | range |
blockCount | 2 | int(10) unsigned | range |
blockSizes | 4,4 | longblob | |
chromStarts | 0,11197 | 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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585 | AWUT01012676 | 5593 | 16794 | repeat_region1_TSD | 1000 | + | 5593 | 16794 | 0 | 2 | 4,4 | 0,11197 |
585 | AWUT01012676 | 61580 | 64877 | repeat_region2_TSD | 1000 | - | 61580 | 64877 | 0 | 2 | 4,4 | 0,3293 |
585 | AWUT01013263 | 12911 | 20672 | repeat_region3_TSD | 1000 | + | 12911 | 20672 | 0 | 2 | 4,4 | 0,7757 |
585 | AWUT01013263 | 21503 | 26968 | repeat_region4_TSD | 1000 | - | 21503 | 26968 | 0 | 2 | 4,4 | 0,5461 |
585 | AWUT01013263 | 63302 | 69177 | repeat_region5_TSD | 1000 | - | 63302 | 69177 | 0 | 2 | 5,5 | 0,5870 |
585 | AWUT01013449 | 164 | 3568 | repeat_region6_TSD | 1000 | - | 164 | 3568 | 0 | 2 | 4,4 | 0,3400 |
585 | AWUT01013449 | 11559 | 24226 | repeat_region7_TSD | 1000 | - | 11559 | 24226 | 0 | 2 | 4,4 | 0,12663 |
585 | AWUT01013449 | 42942 | 55722 | repeat_region8_TSD | 1000 | - | 42942 | 55722 | 0 | 2 | 4,4 | 0,12776 |
585 | AWUT01014064 | 45001 | 53624 | repeat_region9_TSD | 1000 | - | 45001 | 53624 | 0 | 2 | 4,4 | 0,8619 |
585 | AWUT01014088 | 3388 | 7395 | repeat_region10_TSD | 1000 | + | 3388 | 7395 | 0 | 2 | 9,9 | 0,3998 |
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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. suzukii 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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