More on Perl and sequence alignment
To present more examples of Perl programmes.
To describe methods for constructing multiple sequence alignments.
To introduce suffix trees and their relationship to suffix tries.
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;
understand the sum of pairs method for scoring multiple alignments;
understand how multi-dimensional dynamic programming can yield an
optimal multiple sequence alignment;
understand the Feng-Doolittle algorithm for progressive multiple
know how to draw a suffix tree for a given string.
The lecture handout, featuring some of the lecture slides, is
The Feng-Doolittle algorithm for progressive multiple sequence alignment is
Feng, D.F. and Doolittle, R.F. (1987)
Progressive sequence alignment as a prerequisite to correct phylogenetic trees.
J. Mol. Evol., 25, 351-60
Wikipedia entry for
Last Modified: 15 February 2012
by Graham Kemp