CPS 006G, Fall 2004, Shotgun Simulation

In this assignment you'll write a simple version of a program that reconstructs the DNA/Genome from the sequenced strands that result from shotgun sequencing. In the description below, you can assume the original DNA to be sequenced was cloned several times and that all of the clones were broken into sequenceable-sized chunks via various techniques. Essentially the program you'll work with first receives a list of different-sized sequences that are the results of the laboratory shotgun process. Your program must construct the original sequence from the pieces.

Outline

The basic operations your program must do are described here.
There's a first step you must program to master the basic algorithm. In this program you can assume the data is already in an ArrayList (you'll need to create some data to practice with). Later you'll read the data from either a file or a URL.
For the first part you can either check out shotgunI or the biojava version, shotgunII.

Part II/III

Please check out shotgunIII and create a class that implements the IStrand interface. Provide implementations of each required method in the class, though your implementations can be simplistic/not complete. However, your class should compile. Please try to introduce instance fields in the class, e.g., String fields for both name and sequence.

Submit using eclipse and istrand as the name of the assignment. Submit before class on Friday, Oct. 22.

Part IV

Part IV is here

Owen L. Astrachan

Last modified: Sun Nov 21 10:59:05 EST 2004