All vs. All Alignments and Phylogenetic Trees

Goal:

Do an all-against-all pairwise sequence alignment and use the resulting distance and variance matrices to construct a least squares phylogenetic tree.

Databases:

If you are working in a student computer room you directly can open the SwissProt database with following command

> ReadDb('/home/darwin/DB/SwissProt');

Task:

Given are the following entry numbers from the SwissProt database:

75556, 75557, 75558, 75559, 75560, 75561, 75658, 75659, 75803, 75888

For each of the entries extract the protein sequence and the name of the organism (field OS in SwissProt entry). Do an all against all global pairwise sequence alignment Extract the PAM distances and variances into two matrices. Construct the Least-Squares tree, and draw the unrooted version

Hints:

• Use the SearchTag function to extract the organism name used for the labels.
  
• Use the Align function to do the pairwise alignments. The selectors to extract distance and variance are PamDistance and PamVariance, respectively
  
• Use MinSquareTree to construct the phylogenetic tree. The Darwin data structure for phylogenetic trees is explained in ?Tree.
  
• Trees can be  drawn with DrawTree.
  
• The newer Darwin function called PhylogeneticTree can do all the above in one go.