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Algoritmi e Linguaggi per Bioinformatica: Algoritmi (2014/2015)

Program of the project presentations for the summer term 2015

Presenters: Please send me a draft of your slides at most a week before the date, so I can have a look at them and maybe suggest some improvements/correct possible mistakes/warn of possible pitfalls. I will need a final version for the presentation itself; if at all possible, send it to me at the latest the previous day; else bring it along on a USB stick. It's easiest if you bring your own laptop (and make sure you know how to project with it) and organize yourselves so that there is only one laptop per session. If you absolutely need to, then you can use my laptop but only if your slides are in pdf format (there are compatibility problems between Mac-ppt and Windows-ppt).

Audience: Please ask as many questions as possible! Don't worry: otherwise I'll ask them, and mine are definitely harder to answer!

• Mon 8 June 2015, 11:30-13:30 - aula I
  
  1. Semiglobal alignment (Martina De Toni)
  2. k-band algorithm: Comparing similar sequences (Cristina Bacca)
  3. Star alignment heuristic for multiple sequence alignment (MSA) (Giulia Paiardi, Alice Raineri)
  
  
• Wed 10 June 2015, 11:30-13:30 - aula G
  
  1. Exact matching: The Knuth-Morris-Pratt algorithm (Giada Dal Collo)
  2. Exact matching: The Boyer-Moore algorithm (Antonio Gazziero) - moved to July
  3. Introduction to suffix trees (Silvia Malfatti)
  
  
• Thu 11 June 2015, 8:30-11:30 - aula G
  
  1. Introduction to the Burrows-Wheeler Transform (BWT) (Andrei Florea, Daniele Castrovilli)
  2. FASTA (Chiara Campregher)
  3. PAM matrices (Matteo Gelati)
  4. BLOSUM matrices (Daniela Michelatti, Giulia Ambrosini)
  
  

• Wed 22 July 2015, 14:00 - 17:00 - aula G
  
  1. Semiglobal alignment (Andrea Terranera) - to be confirmed
  2. Affine gap functions (Acaynne Lira Zidanes, Mattia Gabrielli)
  3. LCS and LCS distance (Elena Piffer)
  4. q-gram distance (Lorenzo Di Gregorio, Marco Silvestri)
  
  
• Thu 23 July 2015, 14:00 - 17:00 - aula G
  
  1. Optimal pairwise alignment in linear space (Chiara Bertolaso)
  2. Multiple sequence alignment: introduction, SP-score, DP-algorithm (Martina Mazzon)
  3. Multiple sequence alignment: progressive alignment (Giovanni Pasquini)
  4. PAM matrices (Silvia Atanasio, Jessica Insolda)
  
  
• Fri 24 July 2015, 9:30 - 12:30, aula I
  
  1. Suffix trees: Some applications (Stefano Danese)
  2. Maximal matches distance (Daniele Pellegrini, Akim Crescentini)
  3. Exact matching: The Boyer-Moore algorithm (Antonio Gazziero)