How to find a sequence from a txt file?

I'm trying to identify a specific primer sequence from three different text files. I already have this code:

clear;
clc;

% Open the file
fileID = fopen('cDNA1-1.txt', 'r');

% Read the DNA sequence from the file
dna_sequence = strfind(fileID, '%s');

%
DNAsequence=string(dna_sequence)

% Define the primer sequence
primer_sequence = 'TACG';

% Find the location of the primer sequence in the DNA sequence
primer_location = strfind(DNAsequence, primer_sequence);

% Display the location of the primer sequence
if isempty(primer_location)
    disp('Primer sequence not found in the DNA sequence.');
else
    disp(['Primer sequence found at position(s): ', num2str(primer_location)]);
end

However, for some reason my dna_sequence variable is empty, and I keep getting that the sequence is not found in any of the text files. I know that that's wrong, so I need help.

I will include the three txt files along with my code.

Thank you!

Answer 1

[Voss]

The use of strfind here is not correct:

% Read the DNA sequence from the file

dna_sequence = strfind(fileID, '%s');

It looks like you meant to use fscanf:

% Read the DNA sequence from the file

dna_sequence = fscanf(fileID, '%s');

With that change, the code appears to work (but don't forget to fclose!!!!). (Note that the sequence 'TACG' is found in files 2-1 and 3-1 but not 1-1.)

% Open the file
fileID = fopen('cDNA2-1.txt', 'r');

% Read the DNA sequence from the file
dna_sequence = fscanf(fileID, '%s');

% Close the file
fclose(fileID);

%
DNAsequence=string(dna_sequence)

DNAsequence = "GACGCGGCGCAGGCGGCGGGAGTGCGAGCTGGGCCCGTGTTTCGGCCGCCGCCATGGCCGCGGTGGACCTGGAGAAGCTGCGGGCGTCGGGCGCGGGCAAGGCCATCGGCGTCCTGACCAGCGGCGGCGACGCGCAAGGTCCCCTGACAAGCCCACCAGGCCCCCTGCTGAGATGGCTGTGACCCTGGGCTGACCCGCCCAGTGGCACATTGACTCCGCCTGGAGCTGGGGAGACCAGAGAGGCCCTGTGGTTGGACGGTGGCCTGGGTGCGCTGCTCCTGCCCTCTCCTTGCCCTGCCTCAGCTGCTGCCTGCCAGAGGCGTGGCACCTCACCTCACACCTGCTCCCTGCTGCTGAGCCCCACGCCAAGCTGGAGAGCGGATGAGAAGCATGTGTAACCAGGGTAGAGGTCGAGAGTCCTCTCGTGGGGGTCTCCATGTTCAAGGGAGCTGCCGAGGCTTGAGCAGGAGCCCCCAGCAGGAAACTGGCTTTGCCAAGGCCCCCGCTGGGACAGACTGTTTCTTTCACTGCAGTCCTGGGAGCCGAGGGCAAGGGGACAGGAAAGAGGAAGTGACCTCAGAGCCTGGTGGCACCAGCATCATGTCCAGGCTGGGGGGCATGAACGCTGCTGTCCGGGCTGTGACGCGCATGGGCATTTATGTGGGTGCCAAAGTCTTCCTCATCTACGAGGGCTATGAGGGCCTCGTGGAGGGAGGTGAGAACATCAAGCAGGCCAACTGGCTGAGCGTCTCCAACATCATCCAGCTGGGCGGCACTATCATTGGCAGCGCTCGCTGCAAGGCCTTTACCACCAGGGAGGGGCGCCGGGCAGCGGCCTACAACCTGGTCCAGCACGGCATCACCAACCTGTGCGTCATCGGCGGGGATGGCAGCCTCACAGGTGCCAACATCTTCCGCAGCGAGTGGGGCAGCCTGCTGGAGGAGCTGGTGGCGGAAGGTAAGATCTCAGAGACTACAGCCCGGACCTACTCGCACCTGAACATCGCGGGCCTAGTGGGCTCCATCGATAACGACTTCTGCGGCACCGACATGACCATCGGCACGGACTCGGCCCTCCACCGCATCATGGAGGTCATCGATGCCATCACCACCACTGCCCAGAGCCACCAGAGGACCTTCGTGCTGGAAGTGATGGGCCGGCACTGCGGGTACCTGGCGCTGGTATCTGCACTGGCCTCAGGGGCCGACTGGCTGTTCATCCCCGAGGCTCCACCCGAGGACGGCTGGGAGAACTTCATGTGTGAGAGGCTGGGTGAGACTCGGAGCCGTGGGTCCCGACTGAACATCATCATCATCGCTGAGGGTGCCATTGACCGCAACGGGAAGCCCATCTCGTCCAGCTACGTGAAGGACCTGGTGGTTCAGAGGCTGGGCTTCGACACCCGTGTAACTGTGCTGGGCCACGTGCAGCGGGGAGGGACGCCCTCTGCCTTCGACCGGATCCTGAGCAGCAAGATGGGCATGGAGGCGGTGATGGCGCTGCTGGAAGCCACGCCTGACACGCCGGCCTGCGTGGTCACCCTCTCGGGGAACCAGTCAGTGCGGCTGCCCCTCATGGAGTGCGTGCAGATGACCAAGGAAGTGCAGAAAGCCATGGATGACAAGAGGTTTGACGAGGCCACCCAGCTCCGTGGTGGGAGCTTCGAGAACAACTGGAACATTTACAAGCTCCTCGCCCACCAGAAGCCCCCCAAGGAGAAGTCTAACTTCTCCCTGGCCATCCTGAATGTGGGGGCCCCGGCGGCTGGCATGAATGCGGCCGTGCGCTCGGCGGTGCGGACCGGCATCTCCCATGGACACACAGTATACGTGGTGCACGATGGCTTCGAAGGCCTAGCCAAGGGTCAGGTGCAAGAAGTAGGCTGGCACGACGTGGCCGGCTGGTTGGGGCGTGGTGGCTCCATGCTGGGGACCAAGAGGACCCTGCCCAAGGGCCAGCTGGAGTCCATTGTGGAGAACATCCGCATCTATGGTATTCACGCCCTGCTGGTGGTCGGTGGGTTTGAGGCCTATGAAGGGGTGCTGCAGCTGGTGGAGGCTCGCGGGCGCTACGAGGAGCTCTGCATCGTCATGTGTGTCATCCCAGCCACCATCAGCAACAACGTCCCTGGCACCGACTTCAGCCTGGGCTCCGACACTGCTGTAAATGCCGCCATGGAGAGCTGTGACCGCATCAAACAGTCTGCCTCGGGGACCAAGCGCCGTGTGTTCATCGTGGAGACCATGGGGGGTTACTGTGGCTACCTGGCCACCGTGACTGGCATTGCTGTGGGGGCCGACGCCGCCTACGTCTTCGAGGACCCTTTCAACATCCACGACTTAAAGGTCAACGTGGAGCACATGACGGAGAAGATGAAGACAGACATTCAGAGGGGCCTGGTGCTGCGGAACGAGAAGTGCCATGACTACTACACCACGGAGTTCCTGTACAACCTGTACTCATCAGAGGGCAAGGGCGTCTTCGACTGCAGGACCAATGTCCTGGGCCACCTGCAGCAGGGTGGCGCTCCAACCCCCTTTGACCGGAACTATGGGACCAAGCTGGGGGTGAAGGCCATGCTGTGGTTGTCGGAGAAGCTGCGCGAGGTTTACCGCAAGGGACGGGTGTTCGCCAATGCCCCAGACTCGGCCTGCGTGATCGGCCTGAAGAAGAAGGCGGTGGCCTTCAGCCCCGTCACTGAGCTCAAGAAAGACACTGATTTCGAGCACCGCATGCCACGGGAGCAGTGGTGGCTGAGCCTGCGGCTCATGCTGAAGATGCTGGCACAATACCGCATCAGTATGGCCGCCTACGTGTCAGGGGAGCTGGAGCACGTGACCCGCCGCACCCTGAGCATGGACAAGGGCTTCTGAGGCCAGCCATGCCCACGCCCCTCCCCAGCCCCCACCCATGCCAGCGCAGCGCCAGGGCTCAGATGGGGCCTGGGCTGTTGTGTCTGGAGCCTGCAGGCAGGTGGGGGCTGCGTCCCTGCTCAGCCCATCCCCTGCCTCTATCCCTGGCCACCTGCCAGGCCTCCCTCGGGCTGGTGTCTTGAGACCAGCCTGCCAGGCCCTCCAGCAGGAGGACAGAGTGCCCTGGGGCATCCACCTTCCTGCCCAGGGGACGTGGCGCTGTCGGTGTTTGGAGGCTGCTGCCCCCTGGCTTTGGCGCCCCATGGGCCCTCAGCGTCTCCCCATGCTGGGCTCACTACATGGGCCAGCCCTTGCTCTACCTGGCCGGTAGGCTGCTGGCGCCTAGGTTGTGTTGAGAGGGGGATGCCCCTGGCCCTGCCTCACTGTGACCTGCTCCTGCCCACGTGCAGCACCTGTCACCTTTTCTAGAAATAAAATCACCCTGACTGTGGGGTGCATCGGTCTCCGGAGA"

% Define the primer sequence
primer_sequence = 'TACG';

% Find the location of the primer sequence in the DNA sequence
primer_location = strfind(DNAsequence, primer_sequence)

primer_location = 1×6

685 1363 1828 2071 2308 2812

% Display the location of the primer sequence
if isempty(primer_location)
    disp('Primer sequence not found in the DNA sequence.');
else
    disp(['Primer sequence found at position(s): ', num2str(primer_location)]);
end

Primer sequence found at position(s): 685  1363  1828  2071  2308  2812

[Gabriela]

Thank you!

[Voss]

You're welcome!

Answer 2

[John D'Errico]

strfind does NOT read a string from a file! You did this:

% Open the file

fileID = fopen('cDNA1-1.txt', 'r');

% Read the DNA sequence from the file

dna_sequence = strfind(fileID, '%s');

WRONG. You opened the file, but then never read anything from the file. Essentially, you got ahead of yourself.

fileID = fopen('cDNA1-1.txt', 'r');

I'll use fread, which brings them in as ascii. So char will convert them. As well, I'll make it a row vector. (There are many ways we could do this. I'm just grabbing one that works.)

D = char(fread(fileID))';

But note that the file contains carriage returns and line feed characters, so I'll strip them out. Keep only the DNA part.

D = D(ismember(D,'ACGT'))

D = 'TCACTGACCCCACTCCTGAGCATGAACTCTCCTCCCCTCCACTCTGCTGTCAGGTTTTGTCTCCATTGGCCAAGAACCTCTTCCACCGGGCCATTTCTGAGAGTGGCGTGGCCCTCACTTCTGTTCTGGTGAAGAAAGGTGATGTCAAGCCCTTGGCTGAGCAAATTGCTATCACTGCTGGGTGCAAAACCACCACCTCTGCTGTCATGGTTCACTGCCTGCGACAGAAGACGGAAGAGGAGCTCTTGGAGACGACATTGAAAATGAAATTCTTATCTCTGGACTTACAGGGAGACCCCAGAGAGAGTCAACCCCTTCTGGGCACTGTGATTGATGGGATGCTGCTGCTGAAAACACCTGAAGAGCTTCAAGCTGAAAGGAATTTCCACACTGTCCCCTACATGGTCGGAATTAACAAGCAGGAGTTTGGCTGGTTGATTCCAATGCAGTTGATGAGCTATCCACTCTCCGAAGGGCAACTGGACCAGAAGACAGCCATGTCACTCCTGTGGAAGTCCTATCCCCTTGTTTGCATTGCTAAGGAACTGATTCCAGAAGCCACTGAGAAATACTTAGGAGGAACAGACGACACTGTCAAAAAGAAAGACCTGTTCCTGGACTTGATAGCAGATGTGATGTTTGGTGTCCCATCTGTGATTGTGGCCCGGAACCACAGAGATGCTGGAGCACCCACCTACATGTATGAGTTTCAGTACCGTCCAAGCTTCTCATCAGACATGAAACCCAAGACGGTGATAGGAGACCACGGGGATGAGCTCTTCTCCGTCTTTGGGGCCCCATTTTTAAAAGAGGGTGCCTCAGAAGAGGAGATCAGACTTAGCAAGATGGTGATGAAATTCTGGGCCAACTTTGCTCGCAATGGAAACCCCAATGGGGAAGGGCTGCCCCACTGGCCAGAGTACAACCAGAAGGAAGGGTATCTGCAGATTGGTGCCAACACCCAGGCGGCCCAGAAGCTGAAGGACAAAGAAGTAGCTTTCTGGACCAACCTCTTTGCCAAGAAGGCAGTGGAGAAGCCACCCCAGACAGAACACATAGAGCTGTGAATGAAGATCCAGCCGGCCTTGGGAGCCTGGAGGAGCAAAGACTGGGGTCTTTTGCGAAAGGGATTGCAGGTTCAGAAGGCATCTTACCATGGCTGGGGAATTGTCTGGTGGTGGGGGGCAGGGGACAGAGGCCATGAAGGAGCAAGTTTTGTATTTGTGACCTCAGCTTTGGGAATAAAGGATCTTTTGAAGGCCAAA'

strfind(D,'TCAG')

ans = 1×7

50 710 732 819 832 1139 1230

And that would be the locations of that substring in your file.

[Gabriela]

Thank you!