How To Find A Pattern For Consensus Sequences Using Java?

Question

[abhishalovers]

How to find a pattern for consensus sequences using java?

Answer 1

[Medhat]

Simply i think you should learn about regular expiration and apply it on the sequence you have here is a simple tutorial list of how to use regular expiration in java Java Regex Tutorial

Java - Regular Expressions

Guide to Regular Expressions in Java

here is a good book that may help Java Regular Expressions: Taming the java.util.regex Engine

after learning from such tutorial you can form the regular expression that you need to detect consensus sequence you have and apply it.

to read fasta file:

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

import org.biojava.bio.*;
import org.biojava.bio.seq.db.*;
import org.biojava.bio.seq.io.*;
import org.biojava.bio.symbol.*;

public class ReadFasta {

  /**
   * The program takes two args: the first is the file name of the Fasta file.
  * The second is the name of the Alphabet. Acceptable names are DNA RNA or PROTEIN.
  */
public static void main(String[] args) {

try {
  //setup file input
  String filename = args[0];
  BufferedInputStream is =
      new BufferedInputStream(new FileInputStream(filename));


  //get the appropriate Alphabet
  Alphabet alpha = AlphabetManager.alphabetForName(args[1]);

  //get a SequenceDB of all sequences in the file
  SequenceDB db = SeqIOTools.readFasta(is, alpha);
}
catch (BioException ex) {
  //not in fasta format or wrong alphabet
  ex.printStackTrace();
}catch (NoSuchElementException ex) {
  //no fasta sequences in the file
  ex.printStackTrace();
}catch (FileNotFoundException ex) {
  //problem reading file
  ex.printStackTrace();
}
   }
   }

more can be found Help Me To Read The Fasta File Through Biojava.

[abhishalovers]

Thank you for this helpful answer Sir. Wanted to know if there is a way to access fasta files to determine consensus sequence using regular expression?