Schema for LTRharvest - LTR Fragments Identified by LTRharvest
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Database: DkikGB2 Primary Table: ltrdigest_RR_tract Row Count: 163   Data last updated: 2022-10-20
field | example | SQL type | info |
bin | 585 | smallint(5) unsigned | range |
chrom | AFFH02000165 | varchar(255) | values |
chromStart | 6837 | int(10) unsigned | range |
chromEnd | 6853 | int(10) unsigned | range |
name | LTR_retrotransposon1_RR_tract | varchar(255) | values |
score | 1000 | int(10) unsigned | range |
strand | - | char(1) | values |
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Sample Rows
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bin | chrom | chromStart | chromEnd | name | score | strand |
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585 | AFFH02000165 | 6837 | 6853 | LTR_retrotransposon1_RR_tract | 1000 | - |
585 | AFFH02000165 | 18726 | 18739 | LTR_retrotransposon2_RR_tract | 1000 | + |
585 | AFFH02000593 | 11649 | 11659 | LTR_retrotransposon7_RR_tract | 1000 | + |
585 | AFFH02001951 | 8475 | 8483 | LTR_retrotransposon18_RR_tract | 1000 | + |
585 | AFFH02002827 | 5719 | 5734 | LTR_retrotransposon26_RR_tract | 1000 | - |
585 | AFFH02003576 | 5226 | 5240 | LTR_retrotransposon33_RR_tract | 1000 | + |
585 | AFFH02003947 | 23470 | 23480 | LTR_retrotransposon38_RR_tract | 1000 | + |
585 | AFFH02003948 | 14446 | 14463 | LTR_retrotransposon39_RR_tract | 1000 | - |
585 | AFFH02004003 | 5426 | 5434 | LTR_retrotransposon42_RR_tract | 1000 | - |
585 | AFFH02004151 | 1172 | 1182 | LTR_retrotransposon43_RR_tract | 1000 | - |
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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. kikkawai 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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