CSC334 Lab3
Contents
- 1 DNA Sequence Alignment with Processing--A First Approach
- 1.1 Methodology
- 1.1.1 Step 1: Display in the Status Box
- 1.1.2 Step 2: Display a vertical bar between exactly matching symbols
- 1.1.3 Step 3: Translate DNA Sequence 1 when the user presses the key 1
- 1.1.4 Step 4: Translate DNA Sequence 2 when the user presses the key 2
- 1.1.5 Step 5: Keep track of longest subsequence of exactly matching symbols
- 1.1.6 Step 6: Return automatically to best match found
- 1.1.7 Step 7: Animation: make the program shift both sequences and compute the best exact alignment
- 1.2 Resources and Links
- 1.3 Solution program
- 1.1 Methodology
DNA Sequence Alignment with Processing--A First Approach
In this lab you will use a DNA alignment program written in Processing to explore the concept of aligning DNA sequences.
You may want to install Processing on your machine if it is not installed yet, and run through the very good tutorial listed in the resource section at the end to understand the basics of Processing. In this lab, however, we won't use any sophisticated 2- or 3-D graphics. Just moving text.
Methodology
- Open the Processing edit window.
- Copy and paste the following program into the edit window: DNA_Align.pde .
- Save your program as DNA_Align.pde
- Run the program.
- Type + or - to make the sequences move left and right.
- Notice that the number of exact matches is printed in the Processing console.
Step 1: Display in the Status Box
Step 2: Display a vertical bar between exactly matching symbols
Step 3: Translate DNA Sequence 1 when the user presses the key 1
Step 4: Translate DNA Sequence 2 when the user presses the key 2
Step 5: Keep track of longest subsequence of exactly matching symbols
Step 6: Return automatically to best match found
Step 7: Animation: make the program shift both sequences and compute the best exact alignment
Resources and Links
- A good tutorial on Processing can be found here File:ProcessingTutorial.pdf
- The main page for syntax help on Processing is processing.org/reference. A quick way to find information on a given topic in Processing, say on rectangles, is to enter something like this in the Google search bar: site:processing.org rectangle.
