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Help and guidance needs with identification of Transposable elements Kbio The Pipeline 0 07-11-2015 02:03 AM
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Old 09-05-2018, 04:41 AM   #1
bioinfo441
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Default finding Transposable Elements using RepeatMasker

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I have been trying to detect, classify the transposable element in my eukaryotic non-referenced genome, (denovo)

I'm using RepeatMasker to do the job but whenever I run the tools the results shows only simple repeat and satellites.

where I'm trying to detect LTR elements, LINEs, SINES

bases masked: 33282890 bp ( 1.66 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
SINEs: 0 0 bp 0.00 %
Alu/B1 0 0 bp 0.00 %
MIRs 0 0 bp 0.00 %

LINEs: 0 0 bp 0.00 %
LINE1 0 0 bp 0.00 %
LINE2 0 0 bp 0.00 %
L3/CR1 0 0 bp 0.00 %
RTE 0 0 bp 0.00 %

LTR elements: 0 0 bp 0.00 %
ERVL 0 0 bp 0.00 %
ERVL-MaLRs 0 0 bp 0.00 %
ERV_classI 0 0 bp 0.00 %
ERV_classII 0 0 bp 0.00 %

DNA elements: 0 0 bp 0.00 %
hAT-Charlie 0 0 bp 0.00 %
TcMar-Tigger 0 0 bp 0.00 %

Unclassified: 0 0 bp 0.00 %

Total interspersed repeats: 0 bp 0.00 %


Small RNA: 0 0 bp 0.00 %

Satellites: 1 267 bp 0.00 %
Simple repeats: 663679 27953718 bp 1.39 %
Low complexity: 123705 6154714 bp 0.31 %



any idea or suggestions can help me out, please tq
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Old 09-06-2018, 07:56 AM   #2
r.rosati
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Hi! RepeatMasker identifies interspersed repeats by comparing it with predefined sequence libraries. Your species might just have different repeats from the tables that RepearMasker uses. At the same website you will find RepeatModeler, which might fit your needs better, I think...
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Old 09-08-2018, 09:45 PM   #3
bioinfo441
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thanks for the response

what I understand from your replay that I have to create a special library from target genome with Repeatmodeler then run Repeatmasker again?

is there any suggestions for a suitable tool that can scan this element out of the sequence
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