Dear all,
I am not a bioinformatician, and have to admit I am a bit lost in the big world of transposable elements analysis tools...
So here is my question:
I have a sequence of few kb, and was wondering whether I could find an online tool (or something almost as simple as this) to check for potential transposable elements or any sequence that could look like a piRNA cluster or precursor (I know these are not fully understood!).
And another question for piRNA experts:
Do you think Piggybac sequences could be recognised as transposable elements by the piRNA machinery and give rise to piRNAs?
Thanks in advance for your precious advises and comments.
Hi Noemie,
You can try to register and query Repbase to find putative TE that match your sequence. Another way to look at this is to download and create a UCSC track with piRNA sequences (which ever you are interested in). This should allow to visualize piRNA abundance genome wide. Then, when you perform a BLAT search, with your query, you can see if it fall in a region that has a lot of piRNAs (putative clusters). If you feel lazy I am pretty sure that piRNA cluster coordinates (based on whatever assembly) are available for you to download. I am not a Drosophila piRNA specialist, but I know that these exist in a repository or in the original papers (anything raging from 2007-to-2009). As per your second question, piggybac is a DNA transposon and those are recognized by piRNAs (at least some of them) so maybe.
I hope this helps.
Good luck.
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