Find a specific characters in a string

Hello, I am trying to I get certain amino acids from my sequence, however, my output only gives that there are 3 of the amino acids I am looking for but I want it to tell me the amino acid name and create a new string.

I would also want my code to run other larger sequences if need be.

I am not sure if a swich case was the best approach to do this task. Can someone please help me, thank you!

aminoacids = 'MetArgGlyLeuAspTrpAspGlyAsn'
for d = 1:3:(length(aminoacids)-2)
    rgroup = aminoacids(d:(d+2));
    switch (rgroup) 
        case {'Arg', 'Asp', 'Cys', 'Glu','Lys','Tyr'}
            disp(aminoacids)  
    end 
end 

Answer 1

[Stephen23]

C = {'Arg', 'Asp', 'Cys', 'Glu','Lys','Tyr'};
T = 'MetArgGlyLeuAspTrpAspGlyAsn';
R = join(string(C),'|');
A = regexp(T,R,'match')

A = 1×3 cell array
    {'Arg'}    {'Asp'}    {'Asp'}

[Miriam Contreras Castillo]

Thank you Stephen23! Is there also a way to get the first and last amino acid with regexp? I looked at the matlab documentation for regexp but I am not sure how to write it?

[Walter Roberson]

The match is in order, so A{1} and A{end} are the first and last matches.

[Miriam Contreras Castillo]

Thank you! But this only works for cell type data? What if it is just a string?

[Stephen23]

"But this only works for cell type data? What if it is just a string?"

It works for string arrays too:

S = ["Arg", "Asp", "Cys", "Glu", "Lys", "Tyr"];
T = "MetArgGlyLeuAspTrpAspGlyAsn";
R = join(S,'|');
A = regexp(T,R,'match')

A = 1×3 string array
    "Arg"    "Asp"    "Asp"

Answer 2

[Paul]

Hi Miriam

I'm not quite sure what you're looking for. However, transforming everything to strings might offer a path forward via standard Matlab functions and indexing. For example

aminoacids = 'MetArgGlyLeuAspTrpAspGlyAsn';
C = string({'Arg', 'Asp', 'Cys', 'Glu','Lys','Tyr'})
S = string(reshape(aminoacids,3,[]).')

Find all the acids in S that are present in C

S(ismember(S,C))

ans = 3×1 string array
    "Arg"
    "Asp"
    "Asp"