Tools For The Identification Of Transposons

Question

[Anima Mundi]

Hello,

Could you please suggest me a tool capable to recognize transposons among a given set of mammalian sequences?

[Eric Fournier]

You might want to check the reviews mentionned in this question: http://biostar.stackexchange.com/questions/13359/guide-to-working-with-repeated-elements

One of them includes a list of tools which could possibly suit your purpose.

[Anima Mundi]

Oh, thank you; I will gladly check that list.

Answer 1

[Frédéric Mahé]

You could use RepeatMasker or Censor for a preliminary screening.

[Anima Mundi]

Even if I understand the ratio of the approach you propose, I would like to be able to distinguish as robustly as possible transposons from other low complexity regions, so the use of masking algorithms would not help much (I already have candidate regions). Thank you anyway.

[Frédéric Mahé]

RepeatMasker and Censor not only mask regions, they also classify the masked regions into different types, including the different types of transposons (retroviruses, gypsy, copia, ogre, etc).

[Anima Mundi]

I am trying to use Censor (I already used RepeatMasker), and it gave interesting results, so maybe I should have payed more effort in its evaluation from the beginning, sorry for this.

[Frédéric Mahé]

No problem. I'm sure more precise transposon classification tools and databases exist (especially for mammals), but I did not manage to locate one.