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Algoritmi e Linguaggi per Bioinformatica: Algoritmi (2013/2014)

Program of the project presentations for the summer term 2014

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. You can use my laptop only if your slides are in pdf format (there are compatibility problems between Mac-ppt and Windows-ppt); but in any case it's easiest if you bring your own laptop (and make sure you know how to project with it).

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

• Mon 9 June 2014, 14.30-16.30 - aula H
  
  1. DCA for MSA: Multiple sequence alignment with divide and conquer (Nicola Gaburro)
  2. Burrows-Wheeler Transform (BWT) (Lucas Moron Dalla Tor)
  3. Karp-Rabin algorithm for exact string matching (Emiliano Maresi)
  
  
• Tue June 10 2014, 9.30-12.30 (we will prob.ly finish much earlier)
  - aula L (until 10.30), lab Gamma (10.30-12.30)
  
  1. FASTA (Melissa Perfranceschi, Carolina Conter)
  2. BLOSUM matrices (Samuele Cheri)
  3. Pairwise alignment in linear space (Alessandro Baldo)
  
  

Preliminary program for July: still some changes possible!



• Mon 14 July 2013, 9.30 - 12.30 - (aula H)
  
  1. k-band algorithm for comparing similar sequences (Federica Steccanella)
  2. Exact matching: Boyer-Moore algorithm (Damiano Stanzial)
  3. Edit distance and similarity (Lisanna Ghiotto)
  4. PAM matrices (Giuditta Dal Cortivo)
  
  
• Thu 17 July 2013, 9.30 - 12.30 - (aula H)
  
  1. Exact matching: The Knuth-Morris-Pratt algorithm (Maria Carelli)
  2. DP for edit distance (Jessica Speri)
  3. Maximal matches distance (Flavio Matassoni)
  4. Affine gap functions (Stefano Serra, Michela Deiana)
  
  
• Mon 21 July 2013, 14.00 - 17.00 - (aula H)
  
  1. WOTD algorithm for suffix tree construction (Paola Fassan, Valentina Tonin)
  2. Longest common subsequence (Maria Chiara Lanfreducci)
  3. General gap function (Stefano Massella)
  
  
• Tue 22 July 2013, 9.30 - 12.30 - (aula H)
  
  1. q-gram distance (Elena Trombin, Chiara Ravagnini)
  2. Applications of suffix trees (Antonio Demaio)
  3. Suffix arrays (Monica Marchetto)