* Questions and answers

* 1. Program to create oligo motives: oligos.pl
* 2. Program to scan genome for occurrence of oligos: oligo_scan.pl
* 3. Program to plot table plotscan.pl

* Homework assignment:

-Modify oligos.pl so that it is more flexible and uses user input to decide for how big an oligo it should calculate all possible combinations. As usual, there are many approaches to do this. An ugly one would be to write a script that writes the oligos.pl program, and then executes it (similar to what plotscan is doing with the plot.p file).

-Why do some oligos consistently have zero strand bias?

- Can you find a way to make the oligos.pl program more efficient? At present the program calculates all possible oligos of size n and their complements. As a result every oligo nucleotide occurs twice. Overall the analyses would work twice as fast, if one would list every oligo only once, as $oligo or as $oligoc.

-Write a program that goes through the oligo_scan output and reports the oligos with the highest amount of strand bias.

-Modify oligoscan.pl so that it works on all *.nfa files present in a directory, and writes the output tables into files that have the genome name as the first part, and the extension tbl. E.g. the analysis of the genome Ecoli.nfa should be stored into Ecoli.tbl, the analysis of B.subtilis.nfa should be stored in B.subtilis.nfa.
Modify the the plotscan.pl program accordingly.