Welcome to the OCDAP Wiki!

What is OCDAP?

The project to create an Online Collaborative DNA Analysis Program (OCDAP) began in August 2014 by Katherine Nelson, an undergraduate research student at Meredith College, and her two project mentors, Dr. Barrett Koster (computer science) and Dr. Jason Andrus (biology). OCDAP is an online, open-access program that provides user-friendly visualization of restriction enzyme cut sites in a DNA sequence. By the end of May 2015, OCDAP could do the following:

• Allows users to input the gene ID of a DNA sequence from the National Center for Biotechnology Information (NCBI) website into a form
• Allows users to select a restriction enzyme from a list compiled from BioEdit (c) Tom Hall.
• Retrieves the DNA sequence associated with the entered gene ID from NCBI and edits it for analysis
• Finds all instances within the DNA sequence where the selected restriction enzyme can cut
• Lists the user's input information at the top of the result page
• Draws the DNA sequence into primary lines of about 93 nucleotides (or 31 codons) on the result page, along with its complementary strand directly underneath each primary line
• Highlights the restriction cut site on the primary strand in blue, and on the complementary strand in yellow
• Draws a gray arrow through the restriction cut site; the shape and direction depend on the restriction enzyme selected
• If no cuts can be made, writes an error statement on the result page that no instances of the selected restriction cut enzyme could be found in the DNA sequence.

The code is comprised of HTML5, Javascript, and PHP.

How do I join the project?

There are still many improvements that need to be made to this project, which will be listed on another page of this wiki. If you would like to contribute to this project, please feel free to contact any of the people listed below:

Katherine Nelson - [email protected]

Barrett Koster - [email protected]

Jason Andrus - [email protected]