Re: [DIYbio] Re: Anand - Lets FFT that wet stuff ...

HI Daniel,

Thanks for your reply.

point 1.
I note your point that DNA encoding should not be over-simplified. And I agree in principle with this.
However, the type of encoding used will depend on the question being asked.
And for the purpose of my research question, I don't think anything beyond already utilized encoding(s) need to be implemented - i.e. no need to re-invent the proverbial (research) wheel.

point 2.
This project is neither a safari nor an expedition.
Work done previously as research paper citations or body of work from 2 separate research groups are linked below.

point 3.
Due to the real possibility of nauseatingly detailed discussions between us ensuing, your suggestion about moving future email discussions off the forum unless is a good one, unless anyone else expresses interest to be included in their reply to my reply here.

Being a molecular geneticist and genomicist, performing digital signal processing is way outside my skillset i..e this is NOT a DIYbio project for me. Therefore, I looking for collaborator(s) with the skillset complementary to mine. Hope that provides complete context for  this email thread thus far.

Lin, J., Wei, J., Adjeroh, D. et al. SSAW: A new sequence similarity analysis method based on the stationary discrete wavelet transform. BMC Bioinformatics 19, 165 (2018). https://doi.org/10.1186/s12859-018-2155-9

Kamal, N.A.M.; Bakar, A.A.; Zainudin, S. Optimization of Discrete Wavelet Transform Feature Representation and Hierarchical Classification of G-Protein Coupled Receptor Using Firefly Algorithm and Particle Swarm Optimization. Appl. Sci. 2022, 12, 12011. https://
doi.org/10.3390/app122312011

Farman Ali, Omar Barukab, Ajay B Gadicha, Shruti Patil, Omar Alghushairy, Akram Y. Sarhan, "DBP-iDWT: Improving DNA-Binding Proteins Prediction Using Multi-Perspective Evolutionary Profile and Discrete Wavelet Transform", Computational Intelligence and Neuroscience, vol. 2022, Article ID 2987407, 8 pages, 2022. https://doi.org/10.1155/2022/2987407

https://scholar.google.co.in/citations?user=LJR5DfUAAAAJ&hl=en

https://scholar.google.com/citations?user=YzfenUAAAAAJ&hl=en

I look forward to your response. Thanks in advance.

Best,

Anand K.S. Rao, Ph.D.

On Sunday, March 12, 2023 at 1:00:11 PM UTC-4 dank...@gmail.com wrote:

HI Anand,

I'm glad I asked, not just to inform me, but this gets the idea(s) out for everybody.

Doing time series to FFT is one of the few algorithms I haven't been able to apply well ! When I was 'young' I tried it in Fortran and always ran out of dynamic range, it was always miss-calibrated and was more like a 'tone detector' then a histogram. As a hint when that was, it was in Fortran on a Data General Eclipse.

-anyway-

I'm assuming you suggest an x-form into the frequency domain, then matching somehow is in your scope of work on this.

Offhand, I don't think that seems like it will do much; but obviously you are on a larger safari then one assumption I made here. I do also like to be wrong. I am sure it is worth doing.

The scope of "DIY" here logically includes a lot of comp sci as opposed to wet chemistry, obviously.

Esp since this forum has relatively little traffic ( sadly ) ... how about poking up more here. I can maybe do something helpful. If its burdensome volume wise we can continue elsewhere. This gets the nuts and bolts of what your considering out to others.

I could maybe write some programs, etc who knows.

One aspect is surely it's good stuff for base pairs to be considered as actionable including there X Y Z and methylation, etc not just a string of five characters... Wrapping on histones, etc all sort of epigenetics needs more attention to 3D xNA. This "If it's not making a protein, its junk" idea is NOT DEAD !!!

Q1: Do you think an end user accessible notation combining B.P. and Cartesian positions in some duality motif, is desirable but weirdly absent ? 

Regs,

Daniel B. Kolis

my ref: Anand, diy, nafl, 12 Mar 2023

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