This text is no longer updated. However, self-assessment questions
have finally become available in April 2001. Moreover, the text may be referenced as follows:
G. Fuellen, Multiple Alignment. Complexity International 4, 1997.
URL http://journal-ci.csse.monash.edu.au/ci/vol04/mulali/mulali.html.
The Complexity International version of this text is one single HTML file.
Georg Fuellen
fuellen@dali.mathematik.uni-bielefeld.de, fuellen@Techfak.Uni-Bielefeld.DE
fuellen@ alum.m it.edu
Postscript version (Fig.7 in color, printing may take long !).
Postscript version (Fig.7 in black&white, reduced quality).
A List of WWW Resources.
Please send comments, critique, flames and praise to the author.
Further instructions for obtaining the Solution Sheet are available by sending email to majordomo@lists.uni-bielefeld.de, with no subject line, and the following message body: subscribe vsns-bcd-solutions
Prerequisites. An understanding of the dynamic programming (edit distance) approach to pairwise sequence alignment is useful for parts 1.3, 1.4, and 2. Also, familiarity with the use of Internet resources would be helpful for part 3. For the former, see Chapters 1.1 - 1.3, and for the latter, see Chapter 2 of the Hypertext Book of the GNA-VSNS Biocomputing Course at http://www.techfak.uni-bielefeld.de/bcd/Curric/welcome.html.
General Rationale. You will understand why Multiple Alignment is considered a challenging problem, you will study approaches that try to reduce the number of steps needed to calculate the optimal solution, and you will study fast heuristics. In a case study involving immunoglobulin sequences, you will study multiple alignments obtained from WWW servers, recapitulating results from an original paper.
Revision History. Version 1.01 on 17 Sep 1995. Expanded Ex.9. Updated
Ex.46. Revised Solution Sheet -re- Ex.3+12. Marked more Exercises by ``A''
(to be submitted to the Instructor). Various minor clarifications in content
and style.
Version 1.02 on 25 Jan 1996. Revised sections 1.3 and 2.1.
Version 1.03 on 11 Mar 1996. Fixed the URL for the Clustal Alignments
in 3.4. Various minor changes.
Version 2.0 on 6 Jun 1996. Added link to our very own Java-based "Multiple
Alignment Visualization Tool" (in section 1.3). Clarified section 2.1 -re-
nodes vs paths defining the Carrillo-Lipman polyhedron. Followed
up on the new definition of "Replacement" in Ch.1. Clarified formulas in section 2.2
by adding extra parantheses. Added immunoglobulin WWW resources. Clarified Ex. 53.
Various other improvements, in particular to section 1.3.
Version 2.01 on 21 Jun 1996. Reworded a few paragraphs in section 2 (see
Newsletter Vol.2 No.3, item 4).
Version 2.02 on 27 Jul 1996. Using the term ``polyhedron'' instead of ``polytope''
in section 2.2. Marked Exercises by ``B'' if they have more biological depth.
Version 2.03 on 18 Mar 1997. Added references to alignment methods using
Hidden Markov Models and Gibbs Sampling. Various minor improvements.
Back to VSNS BioComputing Division Home Page.
VSNS-BCD Copyright 1995, 1996.
Georg Fuellen
