Example 3:

How to Plot the Entropy for a Sample

In this example, you will take a sample generate a profile, compute the entropy and plot it.

Convert a Multi-FASTA file into a profile:

In this example, we will convert a multi-FASTA into a profile.

1. Go (cd) into the ANDES/example_data directory.

2. Run Clustalw2 on sequences to generate .aln file

clustalw2 -infile=20090416.fasta -quicktree

This will generate the 20081201.dnd and the 20081201.aln file.

3. Convert .aln file to profile.

../ClustalALN_to_PositionProfile.pl -a 20090416.aln

This will generate the 20081201.prof.

Compute the Variation for a profile:

4. Compute the Normalized Shannon Entropy for the profile:

../Compute_NormalizedShannonEntropy_for_Profile.pl -i 20090416.prof -o 20090416

This will generate the positional entropy file, 20090416.ent

5. Plot the entropy file:

../Plot_Entropy.r 20090416.ent

This will generate an Adobe Acrobat PDF File named 20090416.ent.pdf

6. Visualize the PDF file with your favorite viewer:

acroread 20090416.ent.pdf

The results should look something like this:

From this plot you can see that the variation is fairly random along the aligned sequences. There are a couple of peaks around 600-700 and near 1500, that may be interesting.