TE identification & classification via signal processing techniques?

Question

[gnmcsbnfrmtcsclb]

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).

• Spectral Clustering Algorithm On Protein Sequence @ https://www.biostars.org/p/14588/ (Dead end)

• Fft Appropriate For Multiple Sequence Alignment But Not Mapping @ What Makes Fft Appropriate For Multiple Sequence Alignment But Not Mapping?

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

Answer 1

[lkianmehr]

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

[gnmcsbnfrmtcsclb]

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!