Skip to main content
14 votes

Are there any RepBase alternatives for genome-wide repeat element annotations?

Dfam has recently launched a sister resource, Dfam_consensus, whose stated aim is to replace RepBase. From the annoucement: Dfam_consensus provides an open framework for the community to store both ...
Konrad Rudolph's user avatar
7 votes

Are there any RepBase alternatives for genome-wide repeat element annotations?

For pre-existing reliabe TE libraries it is a bit of a mess, because not everybody deposits the species-specific TE libraries to a database like RepBase. And as far as I know DFAM contains only human ...
Jens Bast's user avatar
6 votes
Accepted

How can I use Nanopore reads to close gaps or resolve repeats in a short-read assembly?

You might want to look into Unicycler (manuscript with more information can be found here); even though it is supposed to be used with bacterial genomes only, it might work well with a small genome ...
mgalardini's user avatar
6 votes

Counting repeated kmers sequences that match at least x % of reads sequence

The following javascript does what you want. You need node.js to run it. It should be easy to translate the code to Python. I have not carefully tested it. Use with caution. EDIT (response to new ...
user172818's user avatar
  • 6,535
5 votes
Accepted

Is it wise to use RepeatMasker on prokaryotes?

If I understood correctly your question, you want to mask those regions in a (FASTA?) genome. I think you could identify those regions using mummer and mask them using bedtools. ...
mgalardini's user avatar
5 votes

Are there any RepBase alternatives for genome-wide repeat element annotations?

You could use RepeatScout, which has defined repeat libraries for a limited number of species (including human, mouse, and rat). If your taxon is not represented, you can also do de novo repeat ...
Chris_Rands's user avatar
  • 3,948
4 votes

Are there any RepBase alternatives for genome-wide repeat element annotations?

AFAIK Dfam and Repbase are currently the two best sources of (a variety of) TE sequences. In my genome annotations I have used RepeatModeler+RepeatMasker and then later used Repbase+tblastx and Dfam+...
tomato_soup's user avatar
4 votes
Accepted

What does "motif 2 bp or longer" mean?

What's your reference for the definition of STRs? I think it is still ambiguous among the community. Wikipedia states motifs of >=2 bp. However other references include homopolymers as well: Source 1, ...
Giuseppe Narzisi's user avatar
4 votes

Looking for a good tool for repeat masking in long sequences

RepeatMasker can downloaded an run locally. There's then no size limit, though do note that it's quite slow for mammalian-sized sequences (you'll want to split it into chunks and run in parallel in ...
Devon Ryan's user avatar
  • 19.6k
3 votes

Annotatation of transposable elements / transposons / SINE sequences in human

repeatmasker is meant to annotate/mask a genome given a library of known transposable elements. From the project description, I assume you have not done any sequencing on your own. Then, instead of ...
Kamil S Jaron's user avatar
3 votes
Accepted

Finding 2000 bp sequences that occur more than once in the genome

MUMmer includes a repeat-match tool which can do exactly that: ...
Throckmorton's user avatar
3 votes

Looking for a good tool for repeat masking in long sequences

RepeatFinder may suffice by Volfovsky et al. (2001) and is available for download.
Jack's user avatar
  • 31
3 votes
Accepted

Is there any way to align ChIP-seq reads to telomeres?

This paper https://www.biorxiv.org/content/10.1101/728519v1.full examines the mapping of some human telomeric sequences, and indicates that there is something like 130kb missing at the telomeres in ...
Jay Moore's user avatar
  • 1,012
3 votes

Finding transposable elements using RepeatMasker

You need to model the repeats in your de novo genome. See: http://www.repeatmasker.org/RepeatModeler/ and https://www.biostars.org/p/154290/ (from previous answer) You first build a database named "...
story's user avatar
  • 1,573
3 votes
Accepted

TRAL does not find "Phobos result file"

TRAL 0.3.5 has bugs running and parsing Phobos. You can follow progress towards a fix on this issue: https://github.com/acg-team/tral/issues/16 Until the issue is fixed, you should remove Phobos from ...
Quantum7's user avatar
  • 146
3 votes

Are there any RepBase alternatives for genome-wide repeat element annotations?

+1 for taking issue with RepBase. I use the annotations from the Hammell Lab GTFs that they put out with TEtoolkit. It is similar to what you described to be using so this may be a redundant and ...
AntiSocialBehaviourOrder's user avatar
3 votes
Accepted

Finding the location and unit length of repetitive sequences within a long read

I've sorted the visualisation out. Here are three alternative representations of repetitive structures for the same sequence: These were generated using the same R script, callable from the command ...
gringer's user avatar
  • 14.3k
2 votes

Finding the location and unit length of repetitive sequences within a long read

It could be an idea to fragment the long reads into small sequences, like simulating Illumina reads of 150 bp, and then map these small sequences against the original long reads and extract regions ...
Sergio Arredondo's user avatar
2 votes

Are there any RepBase alternatives for genome-wide repeat element annotations?

I know this question is a bit old, but this is still an issue for a lot of researchers not being able to access RepBase. It seems now that the most recent version of RepeatMasker is dependent upon ...
jpalmer's user avatar
  • 121
2 votes
Accepted

Finding transposable elements using RepeatMasker

That's one answer ^, not sure if you NEED to do that, which wouldn't actually classify your elements as LTRs, it would just find repetitive sequences in your new genome (as you discovered). To get ...
tomato_soup's user avatar
2 votes

Aligning ChIP-Seq reads to repeats for downstream peak analysis

This is very good question, but as far as I know there really isn't a good answer. I will attempt to provide some comments and tips. However, I'm trying to do similar with a dataset which may ...
fridaymeetssunday's user avatar
2 votes

Looking for a good tool for repeat masking in long sequences

From: http://meme-suite.org/doc/glam2_tut.html, here's a few tools that do various repeat masking tasks. These tools mask various kinds of repeats: Repeatmasker, Censor, seg/pseg/nseg, DUST, ...
rroutsong's user avatar
2 votes

RepeatMasker annotation

RepeatMasker comes with a buildSummary.pl script. You can input the .out file from your RepeatMasker run and there is a flag to enter your species e.g. ...
Tane's user avatar
  • 31
2 votes

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

Would advise doing Denovo identification method structure-based. Then use these public databases ( RepBase, Dfam ) to look for high similarity or homology exploration, this possibility if your ...
M.Bioinfo's user avatar
  • 376
1 vote

Where to find the homopolymer regions bed file for Hg002 genome?

If you click through on UCSC you can get to the UCSC source files for hg002. ...
Maximilian Press's user avatar
1 vote

Are there any tools for discovering tandem repeats around a variant in a VCF file?

The old program for doing this last updated in 2016 is Tandem Repeat Finder (TRF) here. This will not find a microsatellite sequence at a given variant, but instead find all tandem repeats in the ...
M__'s user avatar
  • 12.6k
1 vote
Accepted

Are there any tools for discovering tandem repeats around a variant in a VCF file?

After researching a bit, I found a couple of tools that take as input BAM files. I did not test them yet: GangSTR lobSTR hipSTR Tandem Repeat Finder (thanks to Michael G.'s answer) If I find more ...
user324810's user avatar
  • 1,125
1 vote

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

Back in the Day™ RepeatMasker[1] was the go-to tool everyone used for TE annotation in eukaryotes. At the time, the RepBase database from GIRI[2] (license required) was the de facto database ...
Daniel Standage's user avatar
1 vote
Accepted

RepeatMasker annotation

After long years of just conceptual knowledge of what the software does, I was dealing with RepearMasker this week. So, I am not entirely sure I am correct, but ...
Kamil S Jaron's user avatar
1 vote

Finding transposable elements using RepeatMasker

In case someone finds this years later: OP's problem was the use of the "-noint" flag. It stands for "no interspersed", so the OP explicitly asked RepeatMasker NOT to look for ...
evoecogen's user avatar

Only top scored, non community-wiki answers of a minimum length are eligible