Essay

An essay on a topic in Bioinformatics is one of the grade-improving assignments in this course. In contrast to the computer labs, this assignment is individual!. (The usual code of honour applies.)

• About five pages is probably a reasonable amount of text for this essay. Two pages is clearly too little, and ten pages is likely too much effort in the suggested essay topics. Your own judgment is most often very good!
• I will not accept an essay if you have not handed in a report in the mini-project (also known as lab 4).
• The essay should be delivered on paper and electronically.
• The essay can be handed to me personally or via KTH internal mail (leave it at the Albanova reception desk).

What to write about

Below you have some suggestions for essay topics. They have in common that you read two or more papers and then describe and summarize what they are about. Your essay should answer the following questions, but not that I want a an essay, not a bulletpoint list of answers.

• What bioinformatic problems are the articles about? Why are the problems relevant?
• How do the systems work? What similarities and differences do they have?
• What consequences do the different design decisions have? For example, what type of data can they work on and when is the method inappropriate?
• If you today would choose one of the two methods/systems, which one would you take and why?

If you have your of special interest, you are welcome to formulate your own topic and send to me (Lasse) for consideration. I may be able to suggest literature if needed.

Topics

The articles below links to the publisher's versions and might only be accessible from KTH computers. Contact me if you need help getting paper copies.

1. Compare RIO with OrthoStrapper

How do you judge the reliability of orthology assignments?

• Zmasek CM, Eddy SR (2002) RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics 3, 14
• Storm CE, Sonnhammer EL (2002) Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics 18(1), 92—99

2. Comparing Inparanoid with Synergy

Study two different systems for assigning orthology.

• Remm M, Storm CE, Sonnhammer EL (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 314(5), 1041—1052
• Wapinski I, Pfeffer A, Friedman N, Regev A (2007) Automatic genome-wide reconstruction of phylogenetic gene trees. Bioinformatics 23(13), 549—558

3. Evaluating multialignment programs

This topic is for those who are interested in learning more about multialignment. The papers are about evaluation computer programs for multialignment and it is not the actual alignment software you should focus on, but the methods for comparing them.

• Nuin PA, Wang Z, Tillier ER (2006) The accuracy of several multiple sequence alignment programs for proteins. BMC Bioinformatics 7, 471
• Wong KM, Suchard MA, Huelsenbeck JP (2008) Alignment uncertainty and genomic analysis. Science 319(5862), 473—476

4. Genome assembly

This is a larger and somewhat demanding topic aimed at those interested in genomics. The background is the debate about the first versions of the human genome. The debate was not over with the publications in 2001!

• Cozzarelli NR (2003) Revisiting the independence of the publicly and privately funded drafts of the human genome. Proc Natl Acad Sci U S A 100(6), 3021
• Waterston RH, Lander ES, Sulston JE (2002) On the sequencing of the human genome. Proc Natl Acad Sci U S A 99(6), 3712—3716
• Myers EW et al (2002) On the sequencing and assembly of the human genome. Proc Natl Acad Sci U S A 99(7), 4145—4146
• Green P (2002) Whole-genome disassembly. Proc Natl Acad Sci U S A 99(7), 4143—4144
• Waterston RH, Lander ES, Sulston JE (2003) More on the sequencing of the human genome. Proc Natl Acad Sci U S A 100(6), 3022—3024
• Adams MD et al (2003) The independence of our genome assemblies. Proc Natl Acad Sci U S A 100(6), 3025—3026
• Istrail S et al (2004) Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A 101(7), 1916—1921