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 ...
- 4,895
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 ...
- 71
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 ...
- 3,968
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+...
- 184
4
votes
Difference between genome assembly and genome sequence alignment to a reference to find structural variants
the first being what the 1KGP and SDGP did and sequence the whole
genome, align the reads to the reference genome and end up with a BAM
file.
If you have a well defined reference genome (e.g. human, ...
- 3,968
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 ...
- 5,652
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 ...
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 "...
- 1,613
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 ...
- 121
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 ...
- 386
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 ...
- 184
1
vote
Accepted
TEs vertical or horizontal transfers?
You make a phylogenetic tree of the "host species" and compare it to the phylogeny of the TE's. Homology is not a good idea for evolutionary trees.
There are two snags:
Concerted evolution, the TE's ...
M__♦
- 13k
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 ...
- 5,110
1
vote
How can I predict if the binding site of a DNA-binding protein is located on the promoter sequence of a gene?
You could run FIMO on your entire genome for TFs (transcription factors; DNA-binding proteins) of interest, which gives you predicted binding sites: genomic intervals where those TFs bind, with some ...
- 3,184
1
vote
Accepted
Repeatmasker output table
As far as I can tell, you use the -lib option for species where there is no existing RepeatMaster database. Therefore, all it does is attempt to locate versions of ...
- 10.6k
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 ...
- 11
1
vote
Extract LINE-1 methylation status from WGBS data
Via BEDOPS:
$ bedmap —-echo —-echo-map-id-uniq <(bam2bed < reads.bam) <(rmsk2bed < repeats.rmsk) > answer.bed
- 3,184
1
vote
Extract LINE-1 methylation status from WGBS data
After a more extensive search, I found a useful answer that I'll share in case anyone else wonders how to do this. I'm using MethylKit package for differential methylation expression and it is quite ...
- 405
Only top scored, non community-wiki answers of a minimum length are eligible