Schema for LTRharvest - LTR Fragments Identified by LTRharvest
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Database: DyakCAF1 Primary Table: ltrdigest_PBS Row Count: 122   Data last updated: 2022-10-20
field | example | SQL type | info |
bin | 699 | smallint(5) unsigned | range |
chrom | chr2L | varchar(255) | values |
chromStart | 15015293 | int(10) unsigned | range |
chromEnd | 15015312 | int(10) unsigned | range |
name | LTR_retrotransposon4_PBS | 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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699 | chr2L | 15015293 | 15015312 | LTR_retrotransposon4_PBS | 1000 | + |
735 | chr2L | 19700104 | 19700117 | LTR_retrotransposon7_PBS | 1000 | + |
745 | chr2L | 21015052 | 21015064 | LTR_retrotransposon10_PBS | 1000 | + |
745 | chr2L | 21062415 | 21062428 | LTR_retrotransposon11_PBS | 1000 | + |
747 | chr2L | 21251858 | 21251869 | LTR_retrotransposon16_PBS | 1000 | + |
749 | chr2L | 21625129 | 21625140 | LTR_retrotransposon31_PBS | 1000 | + |
751 | chr2L | 21853524 | 21853536 | LTR_retrotransposon38_PBS | 1000 | + |
752 | chr2L | 21986838 | 21986852 | LTR_retrotransposon44_PBS | 1000 | + |
585 | chr2R | 111868 | 111879 | LTR_retrotransposon63_PBS | 1000 | + |
587 | chr2R | 327912 | 327923 | LTR_retrotransposon70_PBS | 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. 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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