How do i delete introns from a RNA sequence?

Hi, I have a char array, and i want to write a code that looks for specific motifs that start with GU and end with AG, and then delete them from my array. I don't know how many times this motif will be in my array so i need some help in understanding how to write this code..

Thanks!

Answer 1

[BhaTTa]

Sure, let's write a MATLAB script to find and remove motifs that start with "GU" and end with "AG" from a given character array. We'll use regular expressions to identify these motifs and then remove them from the array.

Here's a step-by-step approach:

1. Identify the motifs: Use regular expressions to find all substrings that start with "GU" and end with "AG".
2. Remove the motifs: Replace the identified motifs with an empty string.

clc;
clear all;
close all;

% Example character array
charArray = 'This is a test GUabcAG and another GUxyzAG in the sequence.';

disp('Original Character Array:');
disp(charArray);

% Define the regular expression pattern for motifs starting with "GU" and ending with "AG"
pattern = 'GU.*?AG';

% Find and remove the motifs
charArray = regexprep(charArray, pattern, '');

disp('Character Array after Removing Motifs:');
disp(charArray);

Explanation

1. Example Character Array: Define a sample character array charArray containing some text with motifs starting with "GU" and ending with "AG".
2. Display Original Array: Print the original character array to the console.
3. Define Pattern: Use a regular expression pattern GU.*?AG to match any substring that starts with "GU" and ends with "AG". The .*? part matches any characters in a non-greedy manner, meaning it will match the shortest possible string between "GU" and "AG".
4. Remove Motifs: Use the regexprep function to replace all matched motifs with an empty string, effectively removing them from the character array.
5. Display Modified Array: Print the modified character array to the console to verify that the motifs have been removed.

Notes

• The regexprep function is used for regular expression-based string replacement. It searches for the pattern and replaces it with the specified replacement string (an empty string in this case).
• The .*? in the pattern ensures that the match is non-greedy, so it stops at the first "AG" after "GU".
• This approach works for any number of occurrences of the motif in the character array.