Hello,
Could you please suggest me a tool capable to recognize transposons among a given set of mammalian sequences?
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Anima Mundi
You could use RepeatMasker or Censor for a preliminary screening.
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.
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).
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.
No problem. I'm sure more precise transposon classification tools and databases exist (especially for mammals), but I did not manage to locate one.
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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.
Oh, thank you; I will gladly check that list.