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{\large Tik-61,181: Bioinformatics} \hfill Kaski,Mannila,Nikkilä\\ 
{\large Exercises 2 (part 1), Autumn 2000}

In essay type answers try to answer briefly and concentrate on
relevant issues. It is assumed that the assistant will need only
reasonable amount of time when decoding the answers. If the opposite
occurs, it may affect your grade.

The maximum length of an answer to one question is one page. If you make
some proofs or simulations they can be included as appendixes.  Every
answer will be evaluated with the scale \{0:failed, 3:accepted,
5:accepted with distinction\}. In order to pass the course you need at 
least grade 3 for 60\% of the exercises. In order to pass with
distinction you need to return 95\% of the exercises, and to get the
grade 5 for most of them.

The deadline of the exercises is 31.1.2001.


%Moi: Tässä olisi tehtäviä suurimpaan osaan esitelmistä. Lopusta jäi
%muutama katsomatta, toivottavasti ehdit vilkaista.

%Nuo "too easy":t voisi ehkä jättää lopulliseenkin kuvaukseen?

%Sami

%-----
\begin{itemize}

\item[a)]Too easy; smooth start: SM, Ch.7, Ex. 13.

\item[b)]Easy again: SM, Ch.8, Ex. 2 (Give a \_new\_ example.)

\item[c)]DEKM: Ex. 9.10

\item[d)]DEKM: Ex. 10.4

\item[e)]SSK, Ch. 11: The authors propose a method for computing a substituting
matrix for amino acids. Characterize the differences from the PAM
matrices. Comment the proposal. Where would you use each?

\item[f)]Explain SSK, Ch. 12, eqn (2) (p.242). Use at most 1 page.

\item[g)]Paper by Chen et al (regulatory networks): Try to justify the Maximum
gene regulation problem.

%SSK: Ch. 14: Voisi ehkä jättää väliin.


\item[h)]Paper by Tamayo et al: "Translate" the SOM algorithm to the more
familiar notation (see, e.g.,
http://www.cis.hut.fi/research/som-research/som.html).
%\item[i)]SSK: Ch. 15: Löytyisikö joku yksinkertainen Bayes-verkko-tehtävä
%labrasta? Erkkihän piti sellaisen kurssin vastikään?
\end{itemize}
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