The program to search for strand-bias (see class8) was modified as follows:

• instead of ploting the results from the analysis using gnuplot, a program called scantable.pl goes through the output of oligo_scan.pl and calculates for each oligo the maximum strand bias. (To figure out what this means, it helps to look at the output of the plotscan.pl script - class8, what I call maximum oligo stand bias is the difference along the y-axis for the maximum and minimum value for each curve.)
• oligo.pl was replaced by oligos2.pl. Before you run oligoscan, a list with all oligo pairs (oligo paired with its inverse complement, always 5' to 3') of the selected size needs to be in the same directory. These tables are created with oligo2.pl. Also the program oligo_scan.pl needs to be modified to read in the oligos form the correct file, and to compare these to the correctly sized oligo motifs from the genome (see comments within oligo_scan.pl).
• all three programs now use a command line variable to denote the size of the variable or the file to work on
• a master.pl script now scans the directory for genomes (fasta formatted sequences with the extension *.nfa). For each genome the master script calls oligo_scan.pl and scantable.pl. The results are printed onto the screen and into a file that is called oligo_bias.name_of_genome.

* Homework assignments:

Read through the different scripts to understand what is going on (compare to class8).

Run the master.pl script on at least 3 genomes (see hw5 on where to find the genomes, and question below to choose appropriate genomes; in selecting appropriate genomes keep in mind that the individual lists are "incomplete", e.g., the listing of completed "microbial genomes" does not contain some (any?) archaea). Interpret your results!

Repeat the analysis with differently sized oligos (please feel free to modify oligo_scan.pl to make this possible without rewriting the code).

** Is there a limit to how large one could make the oligos? Why would it be meaningless to calculate the bias for a 30mer?

** Do different organisms have the same or similar oligo strand bias? How quickly does the bias change (with respect to the oligo sequence), when one moves to less related organisms. Possible questions to address: Do archaea have the same bias as bacteria? How about genomes for the same species or the same genus?

** To what extent can the oligo starnd bias be explained by the nucleotide stand bios? Can one calculate how big an oligo bias should be expected from a given single nucleotide bias?