# 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 tables. Further, I used a different -species option each time, but Annotation results contain only short and simple repeats.

Do I have to create a unique library to detect them?

The command I used:

./RepeatMasker -no_is -noint - species mammal Genome.fna


Results:

sequences:         32573
total length: 2004063690 bp  (1981588036 bp excl N/X-runs)
GC level:         41.28 %
bases masked:   33282890 bp ( 1.66 %)
==================================================
number of      length   percentage
elements*    occupied  of sequence
--------------------------------------------------
SINEs:                0            0 bp    0.00 %
ALUs            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 %

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 %
==================================================

• is there any alternative or suggestions for a tool that accomplishes this task, scan the sequence and detect these Elements Sep 9 '18 at 5:51
• Welcome to Bioinformatics. Could edit the question to add your comment to the body of the question? Also could you clarify what do you mean with different species and options ? Are you studying a mammal organism or not?
– llrs
Sep 10 '18 at 8:31
• Maybe use something like RepeatScout to build a library for RepeatMasker, relevant bioinformatics.stackexchange.com/a/347/104 Sep 10 '18 at 11:04
• looks like this can a solution for your problem biostars.org/p/154290 Sep 11 '18 at 11:08
• what I meant by different species . its an option in Repeatmasker to look under a specific range of species. I'm studying eukaryotic sequence so I thought mammal species could be the closest. Sep 17 '18 at 12:30

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 them classified one standard approach is to use evidence of homology to sequences of LTR elements with classifications already, and you can get those in Repbase. If you want to download Repbase, you have to sign up for an account with GIRI but I think they give to anyone who asks. Then you can download the section of Repbase you're interested in (e.g. the whole thing, LTR, DNA-TE, ...) and provide the path to the downloaded library (in FASTA format I think) using -lib, like

RepeatMasker -lib Repbase_LTR.fa genome.fa

If you want to check out my approach to classification by homology you might find some ideas you'd like to try. I used Dfam+nhmmer and Repbase+tblastx to identify evidence for LTR retrotransposon classification.

My software pipeline is available as open-source software. If you want detailed high-quality annotations of LTR retrotransponsons, PhyLTR will automatically annotate putative protein-coding sequence regions, classify them, and remove false-positives like a tandem array of DNA TEs which look like LTR-Rs (good diagram of LTR-R false positives here: https://github.com/oushujun/LTR_retriever/blob/master/Manual.pdf)

Phylogenetic Analysis of LTR retrotransposons https://github.com/mcsimenc/PhyLTR

• This is indeed an interesting approach. Do you have any comments on the actual homology or sequence conservation of different repetitive element "entities" across multiple species? Also wouldn't the approach you mention miss non-LTR TEs? LINE-1 elements are the most abundant TEs in humans but not have LTRs. Feb 28 '19 at 0:47
• I'm not sure what you're thinking of exactly, but I can say that in the all plant genomes I have annotated using this approach resulted in clusters of "Gypsy" "Copia" elements where domain content and organization independently affirmed their classification as such. Also some lower-level "taxa" like Ogre elements were recognizable by domain architecture. This work is meant for LTR elements only. It would work fine for metazoan endogenous retroviruses and LTR retroviruses, but not for LINEs. I think the author of the post mentioned LTRs in the original post on stackoverflow.
– matt
Feb 28 '19 at 2:38
• Dears : i appreciate these knowledge, alight me towards my projects , i have gone far in my analysis using ltrharvest + ltrdigest using 314 protein profiles from Gydb database and trna library obtained using tRnascan, then filtration candidates with protein hits only Remain, now i do have the coordinates and the sequences of the TE class1 , i m trying to classify them into subfamilies ex (copia,gypsy...etc) but i failed , as well as class 2 DNA, MITES and Helitron Results obtained with different pipeline but fail to classify them into subfamilies @matt Mar 5 '19 at 10:11
• @story my project is to report all the Transposable Element in my Draft Genome Class1 LTR and NON-LTR . Class 2 Dna transposons , successfully the LTR structure easily can be detected by Denovo tools , but non-LTR must of the tools need windows operating system like MegaScan non-ltr any suggestions Mar 5 '19 at 10:24
• @matt i did registered to download the database but couldnot find the way to specify only LTR or Dna it comes all together . i tried /// tBlastn - query LTR-filtered_digest.fasta - subject mem.ref -out results /// vrtb.ref its one of many files downloaded from repbase refer to vertebrate but no hits are found Mar 5 '19 at 10:34

You need to model the repeats in your de novo genome.

## build the database