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Codon tables should have start codon statistics #262

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Koeng101 opened this issue Jul 2, 2022 · 5 comments
Closed

Codon tables should have start codon statistics #262

Koeng101 opened this issue Jul 2, 2022 · 5 comments
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easy A quick and easy fix! enhancement New feature or request good first issue Good for newcomers help wanted Extra attention is needed low priority Would be nice to fix, but doesn't have to happen right now/there are more important things
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@Koeng101
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Koeng101 commented Jul 2, 2022

Is your feature request related to a problem? Please describe.
Codon tables should have start codon statistics available for use.

@rkrishnasanka
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Where should we be saving this ?

@carreter
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carreter commented Aug 2, 2023

What do you mean exactly by "start codon statistics"?

@Koeng101
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What do you mean exactly by "start codon statistics"?

I'd like to know, in a given organism's codon table, how many start codons are alternative start codons (for example in E.coli, how many gtg start codons there are vs ATG start codons

Basically a modification of codonTable from

// codonTable holds information for a codon table.
type codonTable struct {
    StartCodons []string    `json:"start_codons"`
    StopCodons  []string    `json:"stop_codons"`
    AminoAcids  []AminoAcid `json:"amino_acids"`
}

to

// codonTable holds information for a codon table.
type codonTable struct {
    StartCodons []string    `json:"start_codons"`
    StopCodons  []string    `json:"stop_codons"`
    AminoAcids  []AminoAcid `json:"amino_acids"`
   StartCodonStatistics map[string]int
}

It's actually not very useful for engineering, it's just something I think is interesting.

@carreter
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This should probably be a method in the Table interface as well.

@Koeng101
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I'd imagine so. As said, this is lower priority because it doesn't matter that much when it comes to building things, but I think it is interesting and shows something about the organisms.

@carreter carreter added enhancement New feature or request help wanted Extra attention is needed good first issue Good for newcomers easy A quick and easy fix! low priority Would be nice to fix, but doesn't have to happen right now/there are more important things labels Sep 16, 2023
@carreter carreter added this to the v1.0 milestone Sep 23, 2023
@carreter carreter moved this from Todo to In Progress in poly development roadmap Sep 23, 2023
@github-project-automation github-project-automation bot moved this from In Progress to Done in poly development roadmap Nov 29, 2023
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Labels
easy A quick and easy fix! enhancement New feature or request good first issue Good for newcomers help wanted Extra attention is needed low priority Would be nice to fix, but doesn't have to happen right now/there are more important things
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