Question

Please develop a Java program that uses this regular expression pattern to search through a FASTA format file containing more than 300 protein sequences all contain the "zinc finger" in their title lines, but not all of them contain this pattern in their sequences. In the output of the program, print out the title line, and the position of the pattern in the sequence, followed by the sequence itself.

Answer 1

To search for a specific regular expression pattern in a FASTA format file using Java, you can use the java.util.regex package. Here is an example program that searches for the pattern 'zinc finger' in both the title lines and sequences of protein sequences.

Step-by-step explanation:

To develop a Java program that searches for a specific regular expression pattern in a FASTA format file, you can use the java.util.regex package, which provides classes for working with regular expressions in Java. Here is an example of a program that searches for the pattern 'zinc finger' in both the title lines and sequences of protein sequences:

import java.util.regex.*;
import java.io.*;

public class FastaSearch {
public static void main(String[] args) throws IOException {
BufferedReader reader = new BufferedReader(new FileReader("file.fasta"));
String line;
Pattern titlePattern = Pattern.compile("^>.*zinc finger.*$");
Pattern sequencePattern = Pattern.compile(".*zinc finger.*");
int position = 1;
while ((line = reader.readLine()) != null) {
if (titlePattern.matcher(line).matches()) {
System.out.println(line);
}
else if (sequencePattern.matcher(line).matches()) {
System.out.println("Position: " + position);
System.out.println(line);
}
position++;
}
reader.close();
}
}

In this example, the program reads each line of the file and uses regular expressions to check if the line matches the title pattern or the sequence pattern. If a match is found, the program prints the corresponding line. The 'file.fasta' should be replaced with the path to your actual FASTA format file.