calculate the number of times each codon appears in a .mat file

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Tahir Detinis Zur 2022-2-28

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评论： Ive J 2022-3-1

Hello,

I have an assignment that involves a given mat file. each row in the file is composed of a DNA sequence and the task is to find for each sequence the number of times each codon appears in it. I have very basic knowledge in MATLAB . Can someone help me solve it?

Thank you!!!

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Answer 1

Ive J 2022-2-28

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https://ww2.mathworks.cn/matlabcentral/answers/1660310-calculate-the-number-of-times-each-codon-appears-in-a-mat-file#answer_906470

在 MATLAB Online 中打开

Maybe this example would help:

% create a random DNA seq
dna_codes = ['A', 'T', 'G', 'C'];
dna_str = string(dna_codes(randi(numel(dna_codes),1, 1000)));
count(dna_str, 'ATG') % count how many times ATG codon (M) has been repeated 
ans = 20

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Tahir Detinis Zur 2022-3-1

Thanks!

But I need to count how many times each codon appears.. Is there a simpler way to do it rather than writing this count(dna_str, 'ATG') for each codon separately?

Thank you!!!!

Ive J 2022-3-1

在 MATLAB Online 中打开

In that case just use:

% create a random DNA seq
dna_codes = ['A', 'T', 'G', 'C'];
dna_str = string(dna_codes(randi(numel(dna_codes),1, 1000)));
res = codoncount(dna_str)
res = struct with fields:
    AAA: 5
    AAC: 7
    AAG: 7
    AAT: 6
    ACA: 5
    ACC: 6
    ACG: 7
    ACT: 2
    AGA: 9
    AGC: 6
    AGG: 5
    AGT: 4
    ATA: 7
    ATC: 9
    ATG: 6
    ATT: 7
    CAA: 3
    CAC: 8
    CAG: 5
    CAT: 2
    CCA: 3
    CCC: 6
    CCG: 7
    CCT: 2
    CGA: 6
    CGC: 7
    CGG: 3
    CGT: 5
    CTA: 6
    CTC: 2
    CTG: 5
    CTT: 5
    GAA: 4
    GAC: 8
    GAG: 10
    GAT: 1
    GCA: 3
    GCC: 6
    GCG: 2
    GCT: 11
    GGA: 8
    GGC: 7
    GGG: 4
    GGT: 4
    GTA: 2
    GTC: 1
    GTG: 3
    GTT: 6
    TAA: 5
    TAC: 10
    TAG: 3
    TAT: 5
    TCA: 8
    TCC: 3
    TCG: 2
    TCT: 12
    TGA: 2
    TGC: 4
    TGG: 6
    TGT: 4
    TTA: 5
    TTC: 7
    TTG: 0
    TTT: 4