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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.

Is there a "definitive" database used with sequences? How "species-specific" would this be?

Furthermore, are there standard algorithms used to find these MGEs? I suspect we don't have a comprehensive database of all possible MGEs, but it may be possible to query against the sequences we do indeed have (or detect any repetitive elements within the genome).

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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 species, the repeats not yet discovered, or deposited in the databases.

If the species well-investigated earlier and the mobile element recognised, I assume it will be a straightforward task using species-specific search via Repeatmasker tool with the -species flag to obtain the MobileElement annotation in the genome.

Let me know if you need any data from Repbase related to your species, i have an entree.

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  • $\begingroup$ Thanks! This is a great answer. For how long has RepBase been subscriber-only? $\endgroup$
    – EB2127
    Feb 25, 2020 at 18:50
  • $\begingroup$ I think the middle of last year $\endgroup$
    – BioInfo
    Feb 26, 2020 at 7:38
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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 recommended for RepeatMasker users. I know de facto isn't necessarily definitive, but it may have been the only public database supported for some time.

It looks like more recent efforts have focused on developing the Dfam database, mirrored after the design of databases like Pfam and Rfam.

[1]Smit AFA, Hubley R, Green P (2013-2015) RepeatMasker Open-4.0, http://www.repeatmasker.org.

[2]Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogentic and Genome Research 110:462-467, doi:10.1159/000084979.

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  • $\begingroup$ Thanks for the answer. So, if I understand correctly, the strengths of the Dfam database over RepeatMasker is that it's more extensive? $\endgroup$
    – EB2127
    Feb 25, 2020 at 18:49

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