https://github.com/camilogarciabotero/biosimplex.jl

Representing BioSequences as Simplex numerical matrix
https://github.com/camilogarciabotero/biosimplex.jl

bioinformatics biojulia biology julia machine-learning

Last synced: 8 months ago
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Representing BioSequences as Simplex numerical matrix

• Host: GitHub
• URL: https://github.com/camilogarciabotero/biosimplex.jl
• Owner: camilogarciabotero
• License: mit
• Created: 2024-02-11T21:53:44.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2024-03-23T22:44:54.000Z (over 2 years ago)
• Last Synced: 2024-04-25T00:03:45.742Z (about 2 years ago)
• Topics: bioinformatics, biojulia, biology, julia, machine-learning
• Language: Julia
• Homepage: https://camilogarciabotero.github.io/BioSimplex.jl/
• Size: 145 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE.md

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  Representing DNA sequences as regular tetrahedrals (Simplex)







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# BioSimplex

> Representing DNA sequences as regular tetrahedrals (Simplex)

This packages has a single public function `biosimplex` that takes a `BioSequence` and returns a *Simplex* representation of a *BioSequence*. The *Simplex* representation is a 3D representation of the *BioSequence* where each base can be represented as unit vectors pointing into a regular tetrahedron (Silverman et al., 1986; Coward, 1997).

## Installation



BioSimplex is a  

    

        

        Julia Language

    

      package. To install BioSimplex,

    please open

    Julia's interactive session (known as REPL) and press ]

    key in the REPL to use the package mode, then type the following command



```julia

pkg> add BioSimplex

```

## Usage

```julia

using BioSequences, BioSimplex

# Create a BioSequence

seq = dna"ATCG"

# Convert the BioSequence to a Simplex representation 

biosimplex(seq)

3×4 Matrix{Float64}:

 0.0   0.942809  -0.471405  -0.471405

 0.0   0.0        0.816497  -0.816497

 1.0  -0.333333  -0.333333  -0.333333

```

## Applications

The *Simplex* representation is useful for to generate a numerical representation of the sequences so that it can be used in machine learning models.

## References

Coward, E. (1997). Equivalence of two Fourier methods for biological sequences. Journal of Mathematical Biology, 36(1), 64–70. https://doi.org/10.1007/s002850050090

Silverman, B. D., & Linsker, R. (1986). A measure of DNA periodicity. Journal of Theoretical Biology, 118(3), 295–300. https://doi.org/10.1016/S0022-5193(86)80060-1