Overview

In this assignment, your program will simulate protein synthesis from DNA. Speci_cally, it reads a DNA string from a file specified on the command line, synthesizes the protein that would be created from this DNA string by the human ribosome, and writes that protein's representation to the standard output stream.

The details of the assignment are specified in the Detailed Requirements section below. The Background section that follows is a short tutorial on the subject of protein synthesis. This assignment will give you experience in using hashes and in processing text using Perl's pattern-matching capabilities.

Background

A DNA string, also called a DNA strand, is a finite sequence consisting of the four lowercase letters a, c, g, and t in any order. The four letters stand for the four nucleotides: adenine, cytosine, guanine, and thymine.

Nucleotides, which are the molecular units from which DNA and RNA are composed, are also called bases.

A special enzyme called RNA polymerase uses the information in DNA to create RNA. A RNA string or RNA strand is a finite sequence consisting of the four lowercase letters a, c, g, and u. The a, c, and g have the same names as they do in DNA, but the u represents uracil. When DNA is transcribed to RNA by RNA polymerase, each thymine base is converted to uracil. Hence RNA strings have u's wherever DNA has t's. RNA in turn serves as a template for the construction of proteins, which are sequences of amino acids. Proteins are synthesized within the ribosomes of living cells by a process called translation. In translation, the RNA string in three-letter groups called codons. Each codon codes for a particular amino acid. For example, guu codes for valine, and uca codes for cysteine. Let us count how many possible three-letter sequences are there in which each letter can be a, c, g, or t. There are four choices for the first letter, four independent choices for the second letter, and four for the third, so there are 43 = 64 different codons. On the other hand, there are only 20 different amino acids. Some amino acids are coded for by multiple codons.

For example, uca, ucc, ucg, and ucu all code for cysteine.

Some codons do not code for any amino acids; they are stop codons. Their purpose is to temporarily terminate protein synthesis while reading the RNA string. There are three such stop codons: uaa, uag, and uga. When a stop codon is reached in the RNA string, protein synthesis is paused. The RNA continues to be read, but amino acids are not created until it sees a special start codon. When it _nds a start codon, translation begins again. This is very much like the way that the Perl compiler treats the comments in your Perl programs. As it reads your program, it translates it into executable instructions until it finds comment start character #. The # tells the compiler to stop compiling, and the next newline character tells it to start compiling again. The # acts like a stop code and the newline, like a start code. The start codon in RNA is aug, which also codes for methionine (Met).

Thus, not all of a RNA string is translated into protein; there are large regions that are gaps in the translation process. As the RNA is read, when a gap is reached, it is skipped over until a start codon is found. These gaps are sometimes much larger than the non-gaps in the RNA. As the ribosome reads the RNA, it splices together the separate pieces that it has translated. As an example, the RNA strand

augguuuauggucucuga

is read as the following sequence of codons

aug guu uau ggu cuc uga

Consulting the tables on page 3 of this assignment, we see that aug is a start codon that codes for methionine

(Met), guu, for valine (Val), uau, for tyrosine (Tyr), ggu, for glycine (Gly), cuc, for leucine (Leu), and uga is a stop codon. Therefore, the sequence Met-Val-Tyr-Gly-Leu is created from this RNA fragment.

Amino acids have long names like cysteine but they also have three-letter names such as Cys, for cysteine, and one-letter uppercase names, such as C for cysteine. It is not always true that the one-letter name is the rst letter of the amino acid's long name. The above sequence would be written MVYGL using the one-letter names. The table on page 3 contains the one-letter names as well.

Detailed Requirements

The program must use the le named on the command line as its input le. Suppose the program were named translate. Then if the user types translate mydna_file the program must read the data in mydna_file. If the input le contains any symbols other than a, c, g, or t, the program should exit with an appropriate error message. The le can be assumed to contain no newlines or white-space characters; the program does not have to check that this is true. (It will be a harder program to write if it is not true.)

The program should read the input le, translate it into RNA, and then transcribe the RNA into a sequence of uppercase one-letter amino acid names.

Translation must always start at the very rst character in the le. Whenever it nds a gap in the RNA, it should start a new line of output. For example, if the RNA string is of the form gapgap, then the proteins coded by seq1, seq2, and seq3 will be on separate lines. The output should contain nothing else, no blank lines, no sentences  just the amino acid sequences, one per line.

For simplicity, the program can assume that the lengths of the gaps are always multiples of three characters.

This is not always the case in reality, but it will greatly simplify the logic within the program. As an example, the input le may have a sequence of length 90 followed by a gap of length 120, followed by a sequence of length 42 and a gap of length 96 and end in a sequence of length 240. The actual input les will be much larger than this.

Program Considerations

Hashes are an ideal data structure for this program. If your program does not use a hash, it is not designed properly. We have not yet learned about functions, but if you want to, you can use functions to simplify your main program. This is not a requirement.

As a reminder, the program must have a proper preamble containing the program name, authorship, date of creation, usage information, a description of the input that it accepts and what it does when given that input.

The program must be self-contained; it cannot depend upon the existence of a data le. When you think through how this program should be designed, you will realize that in order for it to translate the RNA to single-letter amino acid names, it will have to store that mapping somewhere. It must be within the program Testing Your Program All programs must be thoroughly tested before they are released to users. Create some sample input les of a small size and manually gure out what the outputs should be. Run your program and make sure that your output matches the one you manually computed.

Submitting the Solution

Place your completed project in /data/yoda/b/student.accounts/cs132/projects/hwk6 and name it

hwk6_username .pl. Make sure that your le is readable only by you. Make sure that each script has your name in a comment line. Remember, this is your work, and your work alone.