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{\vspace{-0.8cm}
{\LARGE \bf Computational Molecular Biology\\
            Biologia Computazionale\\}
\vspace{6mm}
Romeo Rizzi}
\end{center}

\section*{aims of the course}

The course is meant as an introduction to the field
of Computational Molecular Biology
and as an opportunity
to get in touch with the very spirit
and the methods in Algorithms
and Combinatorial Optimization.\\

\noindent
The main aims of the course,
in order of priority, are:

\begin{itemize}
   \item[1.] Motivate the study of Algorithms
             and Discrete Mathematics techniques
             with applications in Molecular Biology;
   \item[2.] Elucidate the role of algorithms
             in the current practice and research
             in Molecular Biology.
\end{itemize}


\section*{period}

April 2003.

\section*{reference book}

\begin{itemize}
   \item Jo\~ao Setubal and Jo\~{a}o Meidanis.
         {\bf Introduction to Computational Molecular Biology.}
         {\em PWS Publishing Company}
         ITP An International Thomson Publishing Company.\\
         ISBN 0-534-95262-3\\         
\end{itemize}

\vspace{-4mm}
{\bf You can ask for zerox-copies of the above book
at the apposite office (Faculty of Science, close to the Library).}\\

{\bf Puoi richiedere le fotocopie del testo consigliato
qui sopra all'apposito ufficio fotocopie
(Facolt\`a di Scienze, vicino alla biblioteca).}

\section*{program}

\begin{itemize}
   \item[1.] Sequence Comparison;
   \begin{itemize}
      \item[1.1] Local, global and semi-global comparison;
      \item[1.2] Sparing time;
      \item[1.3] Sparing memory;
   \end{itemize}

   \item[2.] Suffix Trees;
   \begin{itemize}
      \item[2.1] Building a Suffix Tree;
      \item[2.2] Selected applications of Suffix Trees;
   \end{itemize}

   \item[3.] Phylogenetic Trees;
   \begin{itemize}
      \item[3.1] The Perfect Phylogeny Problem;
      \item[3.2] Some open phylogeny problems;
   \end{itemize}

   \item[4.] Physical Mapping of DNA;
   \begin{itemize}
      \item[4.1] The Interval Graph Model;
      \item[4.2] The Consecutive Ones Property;
   \end{itemize}

   \item[5.] Genome Rearrangements;
   \begin{itemize}
      \item[5.1] Signed Sorting by Reversals;
      \item[5.2] Unsigned Sorting by Reversals;
   \end{itemize}

\end{itemize}


\section*{language}

Elementary English with Italian gesture.
Everybody is welcome.

\section*{lingua}

Faremo ogni sforzo affinch\`e quello della lingua non
risulti essere un problema per nessuno.

\section*{prerequisites}

 You know that living beings are made up of cells.
 You know what an algorithm is.
 You are interested in Discrete Mathematics.
 After this, still you will need your own motivation and curiosity
 to enjoy your participation to the course.



\section*{timetable (calendario delle lezioni)}

\begin{tabular}{||l|l|l|l|l||}
\hline
Luned\`\i\  7 & 15:30 - 17:30 & aula 7 & Romeo Rizzi & string matching, edit distance \\
Mercoled\`\i\  9 & 15:30 - 17:30 & aula 7 & Pavel & suffix trees \\
Gioved\`\i\  10 & 15:30 - 17:30 & aula 7 & Pavel & suffix trees applications \\
Marted\`\i\  15 & 15:30 - 17:30 & aula 7 & Marco Rospocher & phylogenetic trees \\
Gioved\`\i\  17 & 15:30 - 17:30 & aula 7 & Marco Rospocher & phylogenetic treesphysical mapping \\
Marted\`\i\  22 & 15:30 - 17:30 & aula 7 & Claudio Eccher & physical mapping \\
Mercoled\`\i\  23 & 15:30 - 17:30 & aula 7 & Maria Serafini & genome rearrangement I \\
Gioved\`\i\  24 & 15:30 - 17:30 & aula 7 & Maria Serafini & genome rearrangement I \\
Marted\`\i\  29 & 16:30 - 18:30 & aula 13 & Alberto Caprara? & genome rearrangement II \\
Mercoled\`\i\  30 & 16:30 - 18:30 & aula 13 & Romeo Rizzi & open \\
\hline
\end{tabular}


\section*{exam}

%The course gives 3 credits.
%If you are interested in these credits,
Either you face an oral exam
or you prepare
a set of lectures in which you present some further topic to the class.
The teacher will help you entering this topic.



\section*{web site}

The following is the web-site we built up
for a similar course in spring 2002.

\begin{verbatim}
   http://brenta.dit.unitn.it/~rrizzi/classes/BioComp2003/index.html
\end{verbatim}

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