Computational Biology Program #1

Assigned:	Feb. 3, 2003, Monday
Due:	Feb. 14, 2003, Friday

Objective:To familiarize the student with nucleotides, codons, amino acids, reading frames, and genes.

Input:

• A string of nucleotides {A, T, C, G} of maximum length of 300.

Process:

1. Read in the string of nucleotides (should be able to input string two ways:from input file and random generation).
2. Identify codons.
3. Match codons to amino acids Use an X for the stop codon.
4. Identify any possible genes.

Output:

� Nucleotide Input in Codons, separated by spaces or some other delineation.

� Amino Acid Sequence Use the one-letter association given in Table 1.1, page 3.Separate different sequences found by inserting a return after each stop codon.If a given sequence is a gene, identify it prior to the return.

� Gene identification, if none state No genes found.

Do this three times with different reading frames starting at position 0, 1, and 2.This should be done within the program as a loop.

Submit:

1. Algorithm, neatly hand-written or typed.

2. Hard copy of program (with comments!) & program on disk or emailed to Dr. Kaplan.

3. Two different runs of each type of input.For example, submit two runs where input was via random generation and for each of these generate different output with the three different reading frames. Make sure that at least one run includes a found gene.

You must run your program for the class, so make sure that it is executing properly on a Howard University system.You may program this in any language.