Steps performed with RSAT perl scripts

This directory contains a simple example of utilization of the Poisson-based distance metrics.

In this example, we mixed genes regulated by nitrogen (NIT), phosphate (PHO) and methionine (MET). The list of genes from each group is in the file.

data/NIT_MET_PHO_genes.tab

We retrieved the upstream sequences of these genes.

data/NIT_MET_PHO_up.fasta

These sequences were purged to remove duplicated fragments

data/NIT_MET_PHO_up_purged.fasta

We selected the significantly over-represented oligonucleotides.

data/NIT_MET_PHO_oligos.tab

We counted the number of occurrences of these patterns in each upstream sequence

data/NIT_MET_PHO_oligo_counts.tab

Steps performed with the statistical package R

The R scripts can be found in the directory R-scripts/. To use these scripts, open R and load the scripts in the following order:

1. R-scripts/util.R

2. R-scripts/poisson_distances.R

3. R-scripts/NIT_MET_PHO_dist.R. Before loading the last script, you need to update two rows to indicate the directories on your own machine.