DNA Walk

• Read "Genomic landscapes" by Jean R. Lobry for background
• For every nucleotide, adjust an X or a Y coordinate based on a "compass"

• "walking" Borrelia burgdorferi's genome

1. Get the sequence file into a format Perl can use
2. "Walk" the sequence to determine the XY coordinates
3. Create a CSV file with the coordinates
4. Plot in R or Excel

There are a few different parts to this project.

1. Preprocessing (getting the sequence file)

   input

   fasta filename

   output

   array of nucleotides

2. Walking the genome

   input

   array of nucleotides

   output

   array of X coordinates, array of Y coordinates

3. Creating a CSV file with the coordinates

   input

   array of X coordinates, array of Y coordinates

   output

   CSV file where each row = X, Y

4. Plotting in R or Excel (for completeness)

   input

   DNA walk CSV

   output

   PNG or PDF of the walk

1. Get the sequence file into a format Perl can use (preprocessing)
   1. open the sequence file
   2. read the sequence into an array
   3. close the file
   4. remove the header line and newline characters
   5. create an array of nucleotides, e.g., ('A', 'C', 'G', ...)
2. "Walk" the sequence to determine the XY coordinates
   1. create @x and @y arrays to hold your coordinates
   2. initialize $x[0] and $y[0] to 0 (the origin)
   3. for every nucleotide, assign a coordinate based on the compass
3. Create a CSV file with the coordinates
   • print the coordinates to a CSV
4. Plot in R or Excel