Lecture GK-6

More on Perl and sequence alignment

Aims

• To present more examples of Perl programmes.
• To describe methods for constructing multiple sequence alignments.
• To introduce suffix tries, suffix trees, suffix arrays, the Burrows-Wheeler Matrix (BWM), the Burrows-Wheeler Transform (BWT), and the relationships between these.

Objectives

After this lecture you will be able to:

• use Perl together with other Unix programs, passing input/output to/from your Perl program from/to other programs;
• describe and apply the sum of pairs method for scoring multiple alignments;
• discuss how multi-dimensional dynamic programming can yield an optimal multiple sequence alignment;
• describe the Feng-Doolittle algorithm for progressive multiple sequence alignment;
• draw a suffix tree for a given string;
• find the suffix array for a given string;
• describe how the Burrows-Wheeler Matrix and Burrows-Wheeler Transform are derived;
• describe how the Burrows-Wheeler Matrix and the initial string can be reconstructed from the Burrows-Wheeler Transform.

Supplementary Material

The lecture handout, featuring some of the lecture slides, is available on-line (one per page, four per page).

The Feng-Doolittle algorithm for progressive multiple sequence alignment is described in:

• Feng, D.F. and Doolittle, R.F. (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol., 25, 351-60 (Journal web site)

Wikipedia entry for Suffix tree

Example showing suffix array, the Burrows-Wheeler Matrix, the Burrows-Wheeler Transform, and reconstruction of the Burrows-Wheeler Matrix and the initial string from the Burrows-Wheeler Transform.