COS 126 Assignment 7 Checklist

Goals

Solve a pattern matching problem that arises in computational biology.

Learn to use strings.

More practice with arrays.

Part 0

Copy the following files from /u/cs126/files/gene into an empty directory.

gene.c   prot.1   gene.1   prot.2   gene.2
prot.3   gene.3   prot.4   gene.4

You can copy all the files to the current directory with the command:

cp /u/cs126/files/gene/* .

Part 1 (code and decode)

You can use gene.c as starting point. It handles the input and output. After filling in the missing details, you will be able to execute with the following command:

a.out prot.1 gene.1

Don't accidentally use

a.out gene.1 prot.1

First, get the code function working and debugged. It should read in a character array and return an integer corresponding to the first 3 characters in the array. Think of the 3 characters as a integer represented in base 4, with the mapping a=0, c=1, g=2, and t=3. Your job is to convert this to base 10.

One approach for debugging the code function is to first comment out the portion of code that prints out the results, and replace it with printf statements like the following:

printf("%d\n", code(geneseq));
printf("%d\n", code(geneseq + 3));

The first line should convert the first three characters of the input file gene.1 to the appropriate integer. Similarly, the second line converts the second 3 characters to an integer. Note that geneseq + 3 is the array of gene sequence data starting at the 3rd element; it is equivalent to &geneseq[3]. Since the first 6 characters of gene.1 are attgct, you should get the following output:

15
39

Now, get the decode function working and debugged. The input is an integer between 0 and 63. The function should print out 3 characters corresponding to this integer. Think of the integer converted to base 4. Print out this number using the mapping a=0, c=1, g=2, t=3.

To debug, you can replace the printf statements above with:

decode(15);
decode(39);

This should prodcue the following output:

att gct

To convert from base 10 to base 4, you can use integer division and remainder, or, since the base is a power of 2, right shift and bitwise AND.

Part 2 (matching)

To aid in debugging, initialize each element of genecode[64] to '-' instead of ' '.

You may wish to use the strlen library function.

The solution for the example data in gene.1 and prot.1 is gene.1.ans.

Submission

Use the following submit command:

/u/cs126/bin/submit 7 readme gene.c

The readme file should contain:

Name, precept number, high level description of code, any problems encountered, and whatever help (if any) your received.

Descrbe how you implemented the functions code and decode.

Include the output from the prot.2/gene.2 and prot.3/gene.3 data sets, i.e., the position of the match and the mapping of nucleotide triplets to amino acids.

Enrichment Links

The genetic data is actually cDNA (the coding region of DNA) not DNA; the mapping will be similar to RNA with t replaced by u if you wish to compare with your biology textbook, or the following amino acid table borrowed from EBB 320.

The genetic data is taken from the National Center for Biotechnology.

Kevin Wayne