MATLAB: How i will make function or code for creating pair of 3 element form this string={A, R ,N ,D,C,E,Q,G,H,I,L,K,M,F,P,S,T,W,Y,V}.

amino acidbioinformatictripeptide

i want to make function of Tripeptide composition for 20 basic amino acid{'A', 'R' ,'N' ,'D','C','E','Q','G','H','I','L','K','M','F','P','S','T','W','Y','V'} that give me such out put. 'AAA','RAA','NAA','DAA','CAA','EAA', 'QAA',GAA','HAA','IAA','LAA','KAA', 'MAA','FAA','PAA','SAA','TAA','WAA', YAA','VAA','ARA','RRA','NRA','DRA', CRA','ERA','QRA','GRA','HRA','IRA', LRA','KRA','MRA','FRA','PRA','SRA', ……} i will get 8000 pairs

Best Answer

>> V = 'ARNDCEQGHILKMFPSTWYV';
>> [X,Y,Z] = ndgrid(1:numel(V));
>> P = V([X(:),Y(:),Z(:)]);
>> size(P)
ans =
   8000      3
>> P(1:30,:) % take a look at the first thirty rows.
ans =
AAA
RAA
NAA
DAA
CAA
EAA
QAA
GAA
HAA
IAA
LAA
KAA
MAA
FAA
PAA
SAA
TAA
WAA
YAA
VAA
ARA
RRA
NRA
DRA
CRA
ERA
QRA
GRA
HRA
IRA

If you really want to, you can split each row into the cell of cell array:

C = num2cell(P,2);

C = cellstr(P)

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MATLAB: Function Error / If and elseif statement help

As a replacement for what you have done here, I would suggest using ismember to find the triples that form valid codes. You can even use it to keep track of every marked position so you can see if you forgot to implement any triples.

amino_acid_chain = cellstr(reshape(neucleotide_string,3,[])');
L=false(size(amino_acid_chain));%keep track of replaced codes
library={{'E','GAA','GAG'};...
    {'W','UGG'}};%etc
for n=1:numel(library)
    triplet=library{n}(2:end);%select the triplet(s) from the library (e.g. {'GAA','GAG'})
    letter=library{n}(1);%select the corresponding amino acid letter (e.g. 'E')
    L_current_code=ismember(amino_acid_chain,triplet);%find all positions where the amino acid occurs
    amino_acid_chain(L_current_code)=letter;%replace by the letter code
    L=L | L_current_code;%mark as replaced
end
if any(~L)%shouldn't happen
    error('some code was not implemented correctly')
end

MATLAB: How i change the data from column to rows. it try on transpose but give wrong result.

C = cellstr(P).'
              ^^ you need to transpose if you want a row cell vector.

Best Answer

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MATLAB: Function Error / If and elseif statement help

MATLAB: How i change the data from column to rows. it try on transpose but give wrong result.

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