Schema for LTRharvest - LTR Fragments Identified by LTRharvest
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Database: DsimGB2 Primary Table: ltrdigest_TSD Row Count: 174   Data last updated: 2022-10-20
field | example | SQL type | info |
bin | 593 | smallint(5) unsigned | range |
chrom | CM002910 | varchar(255) | values |
chromStart | 1123749 | int(10) unsigned | range |
chromEnd | 1128803 | int(10) unsigned | range |
name | repeat_region1_TSD | varchar(255) | values |
score | 1000 | int(10) unsigned | range |
strand | + | char(1) | values |
thickStart | 1123749 | int(10) unsigned | range |
thickEnd | 1128803 | int(10) unsigned | range |
reserved | 0 | int(10) unsigned | range |
blockCount | 2 | int(10) unsigned | range |
blockSizes | 4,4 | longblob | |
chromStarts | 0,5050 | 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 | CM002910 | 1123749 | 1128803 | repeat_region1_TSD | 1000 | + | 1123749 | 1128803 | 0 | 2 | 4,4 | 0,5050 |
719 | CM002910 | 17569356 | 17576263 | repeat_region2_TSD | 1000 | - | 17569356 | 17576263 | 0 | 2 | 4,4 | 0,6903 |
744 | CM002910 | 20933130 | 20937438 | repeat_region3_TSD | 1000 | + | 20933130 | 20937438 | 0 | 2 | 4,4 | 0,4304 |
748 | CM002910 | 21394199 | 21398439 | repeat_region4_TSD | 1000 | - | 21394199 | 21398439 | 0 | 2 | 4,4 | 0,4236 |
748 | CM002910 | 21471438 | 21478177 | repeat_region5_TSD | 1000 | + | 21471438 | 21478177 | 0 | 2 | 4,4 | 0,6735 |
749 | CM002910 | 21507795 | 21511749 | repeat_region6_TSD | 1000 | - | 21507795 | 21511749 | 0 | 2 | 5,5 | 0,3949 |
749 | CM002910 | 21545979 | 21557568 | repeat_region7_TSD | 1000 | + | 21545979 | 21557568 | 0 | 2 | 4,4 | 0,11585 |
93 | CM002910 | 21621632 | 21629086 | repeat_region8_TSD | 1000 | - | 21621632 | 21629086 | 0 | 2 | 4,4 | 0,7450 |
750 | CM002910 | 21646174 | 21652954 | repeat_region9_TSD | 1000 | - | 21646174 | 21652954 | 0 | 2 | 4,4 | 0,6776 |
751 | CM002910 | 21781627 | 21785739 | repeat_region10_TSD | 1000 | - | 21781627 | 21785739 | 0 | 2 | 5,5 | 0,4107 |
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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. simulans 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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