Programming Assignment 07
An Introduction to Bioinformatics.
Objective: String manipulation.

Due: Wednesday, April 15th, 10:00 AM

DISCLAIMER : I am a CS person not a Biologist.  I suspect that in trying to explain a little of the science behind this I have made over simplifications or possibly even out-and-out falsehoods.  Forgive me if this is the case.

Overall Background

• DNA consists of a sequence of Nucleotides (also referred to as bases). 
• There are four possible Nucleotides - A, C, G, and T. 
• For more information on how scientists encode DNA and Amino Acids, you might be interested in checking out http://www.sonsorol.org/dag/bioperl/PreSeq.pm.html#Alphabets

Assumptions

• To get started, you may assume that the String provided is a valid String consisting only of the 4 nucleotides listed above.  For example, "CGTAGGCAT" is a legal DNA because it contains nothing but A, C, G, and T.  "CGTAFLCAT" is not a legal DNA because F and L are not part of the base set of nucleotides.

In order to complete this assignment you should create a file called pa07.py which contains the following method (you should complete these in the order listed). 

1. Write the numberOfTimes(sequence,nucleotide) method.

• BACKGROUND :
  • There are times when a scientist may want to know how many times a particular nucleotide occurs in a particular DNA sequence.  This method should provide access to this information.
• ACTION :
  • Add to PA07.py the method called numberOfTimes(). 
  • This method takes one String (sequence) and one character (nucleotide) as parameters. 
  • This method searches the entire DNA sequence one nucleotide (character) at a time testing to see if the current nucleotide is equal to the parameter.  It maintains a running count of how many are found. 
  • This method returns this final count to the client code (the code calling the numberOfTimes() method ).
• LIMITATIONS :
  • You may recall a count() method from Lab12.  You MAY NOT use count() to solve this problem.  You need to write the looping and comparison code yourself.  In essence, you are writing the count method that already exists(). 
  TESTING :
  • Now that we have spent some time talking about testing, I would like you to really think about how to test your code as you write it.  For example, while I said you may assume that sequence is a valid sequence, I did NOT say you should assume that nucleotide is a valid nucleotide.

   

2. Write the generateSecondStrand(sequence) method.

• BACKGROUND :
  • DNA is often represented as a single sequence of nucleotides.  In reality, DNA is a double stranded entity.  However the second strand of the DNA is a simple translation of the first strand - Ts pair with As and Cs pair with Gs. 
  • As an example, below is a simple DNA sequence and it's "Second Strand"
    • DNA Sequence : CACATG
    • Second Strand :   GTGTAC

• ACTION :
  • Add a method called generateSecondStrand(sequence). 
  • This method takes one String (sequence) as a parameter and returns the String which would be the second strand of the DNA sequence receiving the message. 
  • In order to do this, you will need to consider the DNA sequence one nucleotide (character) at a time and generate an output String consisting of the original strand's partner at each corresponding position.
• TESTING :
  • Test with a variety of valid sequences.
  • Do you agree with the results?

   

3. Write the generatemRNASequence(sequence) method.

• BACKGROUND :
  • While this isn't completely accurate, you can consider that the mRNA of a DNA sequence is the second strand of the DNA sequence with each occurrence of the nucleotide T replaced with the nucleotide U.  Using the previous example, this DNS's mRNA sequence would be:
    • DNA Sequence :   CACATG
    • Second Strand :     GTGTAC
    • mRNA Sequence : GUGUAC

• ACTION :
  • Complete the method generatemRNASequence(sequence). 
  • This method takes one String (sequence) as a parameter and returns the String which would be the mRNA sequence of the DNA sequence receiving the message.
  • In order to do this, you will need to first convert the DNA to it's second strand (take advantage of existing code).  Then consider this second strand one nucleotide (character) at a time and generate an output String where you replace each occurrence of T with U and leave all other nucleotides alone.
• LIMITATIONS :
  • Note that I ask you to make this conversion one nucleotide at a time.  Thus, you should be writing the loop yourself and not relying on something like replace().
• TESTING :
  • Test with a variety of valid sequences
  • Do you agree with the results?

4. Write the generateAnAminoAcidSequence(sequence) method.

• BACKGROUND :
  • mRNA can be translated to a sequence of Amino Acids by "breaking" the mRNA sequence into groups of three nucleotides. 
  • Each nucleotide triple (use your discrete mathematics skills to consider why there are 64 of these) translates to one of 20 Amino Acids using the following conversion table (where column one is nucleotide one, columns 2-5 contain nucleotide two, and column 6 contains nucleotide three). 
  • Reading this table we see that nucleotide triple UCG is Ser (Serine) while nucleotide CUG is Leu (Leucine).

 

• For example,
  • DNA Sequence :          CACGTGATC
  • mRNA Sequence :        GUGCACUAG  (or GUG CAC UAG)
  • Amino Acid Sequence : Val His Stop 

  However, most biologists refer to these Amino Acids by a single character value obtained from the table:

Thus, "Val His Stop" would be translated to "VH*"

• ACTION :
  • Add the method named generateAnAminoAcidSequence(sequence). 
  • This method takes a single String (sequence) as a parameter. 
  • This method converts the DNA sequence receiving the message into mRNA (again, use the code you wrote in Step 3). 
  • It then takes this mRNA sequence and divides it into substrings of length 3. 
  • It then translates each nucleotide triple into it's corresponding Amino Acid. 
    • To help you with this, I have written a def called aminoAcidTranslation. 
    • This method  expects a three character String as a parameter and returns the corresponding single character AminoAcid.  To use this method you simply write :

      aminoAcidTranslation( <parameter>)

      (Of course, you replace <parameter> with a three character String.)

       

  • Your job is to figure out how to divide a long mRNA String into nucleotide triples (substrings of length 3), use aminoAcidTranslation to translate these to Amino Acids and return the String which is the complete sequence of AminoAcids for the original DNA.
  • You should not assume that your original String is divisible by 3.  Thus, you will need to be careful at the end of the sequence. You may ignore any "extra" characters at the end of the DNA sequence.  For example, the DNA sequence "CACGT" would translate to mRNA of "GUGCA" and this would translate to the single Amino Acid of "V"
• TESTING :
  • There are several places this method can fail.  Test it carefully.
  • Do you agree with the results?

5. CHALLENGE 1: Write the generateAllAminoAcidSequences() method.

• BACKGROUND :
  • When we look at DNA and mRNA all that we REALLY know is that the sequence is part of a larger sequence.  Thus, when we look at the DNA sequence "CACGTGATC" which translates to the mRNA sequence "GUGCACUAG" all we really know is that this is probably part of a much larger sequence.  In step 4, we made the assumption that this mRNA sequence starts with the letter G, and thus the first triple to convert is GUG which converts to V. 
  • However, if this is just some random subsequence, it may be that the G is the last character of the previous triple.  Thus, the FIRST triple we can process is UGC which would translate to Cys or C. 
  • OR, it might be that both the G and the U are part of the previous triple, and the first triple we can process is GCA which would translate to Ala or A.
  • Therefore, when scientists convert the mRNA sequence to Amino Acid sequences, they normally convert to all the possible sequences.  Thus,
    • DNA Sequence :          CACGTGATCC
    • mRNA Sequence :        GUGCACUAGG 
    • Amino Acid Sequences :
      • VH*  (start with the first letter, consider the first three triples and ignoring the last letter)
      • CTR (ignoring the first letter and considering the next three triples)
      • AL (ignoring the first two letters, considering the next two triples, and ignoring the last two letters)

• ACTION :
  • Add the method named generateAllAminoAcidSequences(). 
  • This method takes a single sequence as a parameter. 
  • This method converts the DNA sequence receiving the message into mRNA (again, use the code you wrote in Step 3). 
  • It then takes this mRNA sequence and considers the three possible ways of dividing it into triples (start with the first character, start with the second character, start with the third character) 
  • For each of these ways, it translates each nucleotide triple into it's corresponding Amino Acid. 
  • Since you can't return Three Strings, you should simply print each of these triples.