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Questions tagged [transposable-elements]

Sequence units in the genome that have the ability to move in the genome, either through a copy-and-paste mechanism or a cut-and-paste mechanism. Transposable elements create interspersed repeats in genomes and can make up a significant proportion of an eukaryotic genome.

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Transposable elements in phylogenetics

I'm very new to phylogenetics and want to build a cladogram from mammal species using pseudogene fragments. The procedure is as follows: Find several query sequences from Gallus gallus of the genes ...
Opossum312's user avatar
1 vote
0 answers
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Sliding window optimisation

I would like to check transposable elements through a genome with a sliding window approach but I am not sure about which window and step size to use. Is there a way to optimise the window size and ...
Balint Biro's user avatar
2 votes
1 answer
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Annotatation of transposable elements / transposons / SINE sequences in human

I need to annotate human genome with different types of information, amongst them: transposable elements. I read about repeatmasker, but what I understood is that it estimates the probability of a ...
Bratten's user avatar
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4 votes
1 answer
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Difference between genome assembly and genome sequence alignment to a reference to find structural variants

I'm trying to determine what the difference and benefits of genome assembly and genome sequence alignments are when trying to identify structural variants or transposons in populations. I've been ...
M4r1n4's user avatar
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1 vote
1 answer
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TEs vertical or horizontal transfers?

After predicting and annotating all the transposable elements. For four related species. Now I would like to find out these predicted candidates found in my costume library, either vertical or ...
M.Bioinfo's user avatar
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2 votes
2 answers
115 views

Is there a "definitive" database for Mobile Genetic Elements?

This isn't quite my speciality, but I've been tasked with finding any evidence of Mobile Genetic Elements (like transposable elements, retrotransposons, bacteriophages, etc.) within some WGS samples. ...
EB2127's user avatar
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0 votes
1 answer
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How can I predict if the binding site of a DNA-binding protein is located on the promoter sequence of a gene?

Is there any computational tool or any other method to predict if the binding site of DNA binding protein is actually located on a promoter sequence?
Charles's user avatar
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1 vote
0 answers
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repeatscout freq table

I'm running Repeatscout. I built the l-mer table called myfile.freq of myfile.fa Can anyone tell me what do they mean the second and third columns produced as output? here I report an example: ...
jonny's user avatar
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2 votes
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Repeatmasker output table

I'm working with an unassembled genome of cephalopod and I would to find transposable elements. My idea is to use repeatscout to generate a library and repeatmasker to find the elements. After ...
jonny's user avatar
  • 171
3 votes
3 answers
914 views

Finding transposable elements using RepeatMasker

I'm using RepeatMasker to detect, classify the Transposable elements. My Input is a eukaryotic non-reference genome. I made a run via RepeatMasker many times to Mask the TEs, but return 0 Annotation ...
M.Bioinfo's user avatar
  • 386
3 votes
3 answers
112 views

Extract LINE-1 methylation status from WGBS data

I've been trying to figure out the correct way of extracting methylation status of particular elements from WGBS data, and found several possible approaches, but would like to discuss which one could ...
Kraken's user avatar
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19 votes
6 answers
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Are there any RepBase alternatives for genome-wide repeat element annotations?

I’m using the RepBase libraries in conjunction with RepeatMasker to get genome-wide repeat element annotations, in particular for transposable elements. This works well enough, and seems to be the de ...
Konrad Rudolph's user avatar