Schema for LTRharvest - LTR Fragments Identified by LTRharvest
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Database: DhydGB1 Primary Table: ltrdigest_TSD Row Count: 104   Data last updated: 2022-10-20
field | example | SQL type | info |
bin | 598 | smallint(5) unsigned | range |
chrom | NWQH01000001 | varchar(255) | values |
chromStart | 1767445 | int(10) unsigned | range |
chromEnd | 1770069 | int(10) unsigned | range |
name | repeat_region1_TSD | varchar(255) | values |
score | 1000 | int(10) unsigned | range |
strand | - | char(1) | values |
thickStart | 1767445 | int(10) unsigned | range |
thickEnd | 1770069 | int(10) unsigned | range |
reserved | 0 | int(10) unsigned | range |
blockCount | 2 | int(10) unsigned | range |
blockSizes | 4,4 | longblob | |
chromStarts | 0,2620 | 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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598 | NWQH01000001 | 1767445 | 1770069 | repeat_region1_TSD | 1000 | - | 1767445 | 1770069 | 0 | 2 | 4,4 | 0,2620 |
585 | NWQH01000004 | 2 | 4940 | repeat_region2_TSD | 1000 | - | 2 | 4940 | 0 | 2 | 4,4 | 0,4934 |
585 | NWQH01000013 | 18857 | 25919 | repeat_region3_TSD | 1000 | - | 18857 | 25919 | 0 | 2 | 4,4 | 0,7058 |
590 | NWQH01000021 | 665714 | 672401 | repeat_region4_TSD | 1000 | + | 665714 | 672401 | 0 | 2 | 4,4 | 0,6683 |
585 | NWQH01000030 | 51631 | 54275 | repeat_region5_TSD | 1000 | + | 51631 | 54275 | 0 | 2 | 4,4 | 0,2640 |
585 | NWQH01000030 | 55355 | 57495 | repeat_region6_TSD | 1000 | + | 55355 | 57495 | 0 | 2 | 4,4 | 0,2136 |
585 | NWQH01000045 | 43589 | 49822 | repeat_region7_TSD | 1000 | - | 43589 | 49822 | 0 | 2 | 4,4 | 0,6229 |
585 | NWQH01000045 | 50807 | 60171 | repeat_region8_TSD | 1000 | - | 50807 | 60171 | 0 | 2 | 4,4 | 0,9360 |
586 | NWQH01000045 | 205743 | 211232 | repeat_region9_TSD | 1000 | + | 205743 | 211232 | 0 | 2 | 4,4 | 0,5485 |
588 | NWQH01000054 | 493177 | 499191 | repeat_region10_TSD | 1000 | - | 493177 | 499191 | 0 | 2 | 4,4 | 0,6010 |
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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. hydei 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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