Hw3.seq TCAGCGAGATGGGAAAGATCACCTTCTTCGAGGACCGAGGCTTCCAGGGC 

Need help with assignment please.

1. The genetic code of any organism consists of three nucleotides, also referred to as codon. Many gene-finding programs rely on translating a piece of DNA sequence in all possible reading frames and looking for the longest uninterrupted region of translation.

Please develop a Java program that reads in a piece of DNA sequence from a sequence file (hwk3.seq) (alternatively you can use the getRandomSeq(long) method of the RandomSeq class to generate a piece of DNA sequence, see week#4 conference), and then print out all the codons in three forward reading frames. Design a method called codon() that can be used to find all the codons from three reading frames. The method will take in an argument, the reading frame (1, 2, or 3), and return an array or ArrayList with all the codons.

All the codons should have three nucleotides, please discard the last one if it does not have three nucleotides. Below is a sample output of the program:

(Here is a reference about DNA sequence reading frames, and you can also used the tool it provided to verify your translation. http://bioweb.uwlax.edu/genweb/molecular/seq_anal/translation/translation.html)

Please enter the file name contains the DNA sequence:

hwk3.seq

The DNA sequence is:

TCAGCGAGATGGGAAAGATCACCTTCTTCGAGGACCGAGGCTTCCAGGGC

Reading frame #1 codons are:

TCA GCG AGA TGG GAA AGA TCA CCT TCT TCG AGG ACC GAG GCT TCC AGG

Reading frame #2 codons are:

CAG CGA GAT GGG AAA GAT CAC CTT CTT CGA GGA CCG AGG CTT CCA GGG

Reading frame #3 codons are:

AGC GAG ATG GGA AAG ATC ACC TTC TTC GAG GAC CGA GGC TTC CAG GGC

2. Please add another method called codon2aa() that modifies the previous program (question #1) to print the corresponding amino acid beneath each codon. Use a single letter representation of the amino acid, and a * for the stopping codon. See below for a sample output.

(Here you can find information on genetic code, and the single letter amino acid translation of the genetic code: http://en.wikipedia.org/wiki/Genetic_code)

Please enter the file name of DNA sequence:

hwk3.seq

The DNA sequence is:

TCAGCGAGATGGGAAAGATCACCTTCTTCGAGGACCGAGGCTTCCAGGGC

Reading frame #1 codons and amino acids are:

TCA GCG AGA TGG GAA AGA TCA CCT TCT TCG AGG ACC GAG GCT TCC AGG

S A R W E R S P S S R T E A S R

Reading frame #2 codons and amino acids are:

CAG CGA GAT GGG AAA GAT CAC CTT CTT CGA GGA CCG AGG CTT CCA GGG

Q R D G K D H L L R G P R L P G

Reading frame #3 codons and amino acids are:

AGC GAG ATG GGA AAG ATC ACC TTC TTC GAG GAC CGA GGC TTC CAG GGC

S E M G K I T F F E D R G F Q G