Schema for LTRharvest - LTR Fragments Identified by LTRharvest |
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Database: DsimGB2 Primary Table: ltrdigest_protein Row Count: 1,963 Data last updated: 2022-10-20
| field | example | SQL type | info |
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| bin | 593 | smallint(5) unsigned | range |
| chrom | CM002910 | varchar(255) | values |
| chromStart | 1124491 | int(10) unsigned | range |
| chromEnd | 1124591 | int(10) unsigned | range |
| name | G-patch | varchar(255) | values |
| score | 0 | int(10) unsigned | range |
| strand | + | char(1) | values |
| thickStart | 0 | int(10) unsigned | range |
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Sample Rows
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| bin | chrom | chromStart | chromEnd | name | score | strand | thickStart |
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| 593 | CM002910 | 1124491 | 1124591 | G-patch | 0 | + | 0 |
| 719 | CM002910 | 17573019 | 17573353 | GAGPOL_ty3gypsy_BMC_Evolutionary_Biology_8_276_2008 | 0 | - | 0 |
| 719 | CM002910 | 17573019 | 17573356 | GAGPOL_ty3gypsyretroviridae_BMC_Evolutionary_Biology_8_276_2008 | 0 | - | 0 |
| 719 | CM002910 | 17573022 | 17573353 | GAGPOL_retroviridae | 0 | - | 0 |
| 719 | CM002910 | 17573025 | 17573353 | RT_caulimoviridae | 0 | - | 0 |
| 719 | CM002910 | 17573028 | 17573353 | GAGCOATPOL_caulimoviridae | 0 | - | 0 |
| 719 | CM002910 | 17573028 | 17573353 | GAGCOATPOL_caulimoviridae | 0 | - | 0 |
| 719 | CM002910 | 17573124 | 17573353 | RVT_1 | 0 | - | 0 |
| 719 | CM002910 | 17573659 | 17573903 | AP_retroelement | 0 | - | 0 |
| 719 | CM002910 | 17573665 | 17573903 | AP_ty3gypsy | 0 | - | 0 |
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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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