Java program to compare 2 seqences of DNA

Write a Java program that will compare two sequences of DNA or Protein and illustrate matching sections in a graphical manner. To do this you must show a two-dimension dot-matrix plot. Every residue in one sequence is compared to every residue in the other sequence. The first sequence runs along the x-axis and the second sequence along the y-axis. In regions where the two sequences are similar to each other, a row of dots

will run diagonally across the plot. If you are comparing a sequence against itself to find internal repeats, you will notice that the main diagonal is a continuous line, since it is a perfect self-match.

The requirements for your application are:

1. There must be two text fields where the two sequences can be entered by the user.

2. There must be a display area for the plot.

3. There must be a Run button which will cause the plot for the two sequences to be displayed.

4. The applet must be written use best programming practices.

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## Deliverables

1) Complete and fully-functional working program(s) in executable form as well as complete source code of all work done.

2) Installation package that will install the software (in ready-to-run condition) on the platform(s) specified in this bid request.

3) Exclusive and complete copyrights to all work purchased. (No GPL, 3rd party components, etc. unless all copyright ramifications are explained AND AGREED TO by the buyer on the site).

## Platform

We have been writing the java scripts in PFE (programmer's File Editor) and running them in MSDOS. Windows 2000

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