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.