Find isn't getting the right index it says: "Error using > Matrix dimensions must agree."

How do I change the find to get the right index in the program that finds stop and start codons to get the longest reading frame?

function [ptn]=seq_transcribe2(x)
y=seq_transcribe1(x);
frames={};
frames={x(1:end) x(2:end) x(3:end) y(1:end) y(2:end) y(3:end)};
starts=[];
stops=[];
allorfs={};
for i=1:3:numel(frames)-2
    for j=1:numel(frames)
  codon= frames{j}([i i+1 i+2])
    if strcmp(codon,'ATG')
    starts= [starts codon];
    end
    if strcmp(codon,'TAA') | strcmp(codon,'TAG') | strcmp(codon,'TGA')
    stops = [stops codon];
    end
    end
end
stops= find(stops>starts,1)
lengthofthisstart=stops-starts
allorfs{end+1}=frames(starts:stops-1)

map=geneticcode;
names=fieldnames(map);
ptn={};

% for i=1:numel(codon)
%     ptn{end+1}=map.(codon{i})
% end
% ptn=char(ptn)';

Answer 1

[Walter Roberson]

It is not self-obvious from the code that the number of starts and the number of stops must be equal. Also, your starts and stops contain the condon characters themselves, not the positions, and all of your stop codons are alphabetically after your start codon so provided that stops and starts are non-empty, the find is going to return position 1.

By the way, you can write

      if strcmp(codon,'TAA') | strcmp(codon,'TAG') | strcmp(codon,'TGA')

as

      if ismember(codon, {'TAA', 'TAG', 'TGA'})

I wonder whether you could replace the loops entirely with some strfind() such as

strfind(frames{j}, 'ATG')

and

sort( [strfind(frames{j}, 'TAA'), strfind(frames{j}, 'TAG'), stfind(frames{j}, 'TGA')] )