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Correct README warnings
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camilogarciabotero committed Jul 8, 2024
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The `GeneFinder` package aims to be a versatile module that enables the application of different gene finding algorithms to the `BioSequence` type, by providing a common interface and a flexible data structure to store the predicted ORF or genes. The package is designed to be easily extensible, allowing users to implement their own algorithms and integrate them into the framework.

!!! warning
> [!WARNING]
This package is currently under development and is not yet ready for production use. The API is subject to change.

## Installation
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The main package function is `findorfs`. Under the hood, the `findorfs` function is an interface for different gene finding algorithms that can be plugged using the `finder` keyword argument. By default it uses the `NaiveFinder` algorithm, which is a simple algorithm that finds all (non-outbounded) ORFs in a DNA sequence (see the [NaiveFinder](https://camilogarciabotero.github.io/GeneFinder.jl/dev/api/#GeneFinder.NaiveFinder-Union{Tuple{Union{BioSequences.LongDNA{N},%20BioSequences.LongSubSeq{BioSequences.DNAAlphabet{N}}}},%20Tuple{N}}%20where%20N) documentation for more details).

!!! note
> [!NOTE]
The `minlen` kwarg in the `NaiveFinder` mehtod has been set to 6nt, so it will catch random ORFs not necesarily genes thus it might consider `dna"ATGTGA"` -> `aa"M*"` as a plausible ORF.
Here is an example of how to use the `findorfs` function with the `NaiveFinder` algorithm:
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