TE identification & classification via signal processing techniques?
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4 months ago

Dear all,

We seek the community's help in figuring out any of the methods described in this researcher's Google Scholar records appear to be valid and practial - shorturl.at/pMPT5.

As a group of biology undergrad students, we are familiar with some bioinformatics. But the tools & techniques mentioned in these papers are commonly used in subject areas we aren't familiar with

  • signal processing
  • electronics & electrical engineering - hence this request for help.

Some of those tools are listed below:

  • Spectral analysis
  • Fourier Transformation (FT)
  • Frequency Chaos Game Signal (FCGS) Encoding
  • Wavelet Transformation
  • Support Vector Machine (SVM)

We did some searches for these topics here on BioStars (very abbreviated list below).

So we do not get lost in these unfamiliar topics, we have these 2 questions please:

  1. Can any of these methods help with better IDENTIFICATION of transposons, specifically Helitron class of TEs?

  2. Can any of these methods help with better sub-CLASSIFICATION of transposons, specifically Helitron class of TEs?

Thank you!

Emily & friends

discovery transposon transform classification • 245 views
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Entering edit mode
4 months ago
lkianmehr ▴ 50

There are programs designed for transposable elements quantification: check out TEToolkit. Programs like TEToolkit can also give you information about families of TEs.

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Thanks but we have not found the usual Helitron discovery tools like HelitronScanner or EA-Helitron to work satisfactorily. If the initial discovery step is not sensitive and specific, then the following classification step is bound to be a waste of time, i.e. garbage in from "discovery" => garbage out after "classification".

Rather than expand on why that is the case, and divert this post, we want to reiterate our question / request from our original post:

Is there anyone here in the bioinformatics community with expertise in using signal processing tools, to evaluate the papers linked in the Google profile, to cross-verify that one or more of these signal processing tool(s) can indeed be used for

  1. Helitron discovery, and
  2. Helitron classification.

Thanks!

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