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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**

- DCA for MSA: Multiple sequence alignment with divide and conquer (Nicola Gaburro)
- Burrows-Wheeler Transform (BWT) (Lucas Moron Dalla Tor)
- 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)

- FASTA (Melissa Perfranceschi, Carolina Conter)
- BLOSUM matrices (Samuele Cheri)
- 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)**

- k-band algorithm for comparing similar sequences (Federica Steccanella)
- Exact matching: Boyer-Moore algorithm (Damiano Stanzial)
- Edit distance and similarity (Lisanna Ghiotto)
- PAM matrices (Giuditta Dal Cortivo)

** Thu 17 July 2013, 9.30 - 12.30 - (aula H)**

- Exact matching: The Knuth-Morris-Pratt algorithm (Maria Carelli)
- DP for edit distance (Jessica Speri)
- Maximal matches distance (Flavio Matassoni)
- Affine gap functions (Stefano Serra, Michela Deiana)

** Mon 21 July 2013, 14.00 - 17.00 - (aula H)**

- WOTD algorithm for suffix tree construction (Paola Fassan, Valentina Tonin)
- Longest common subsequence (Maria Chiara Lanfreducci)
- General gap function (Stefano Massella)

** Tue 22 July 2013, 9.30 - 12.30 - (aula H)**

- q-gram distance (Elena Trombin, Chiara Ravagnini)
- Applications of suffix trees (Antonio Demaio)
- Suffix arrays (Monica Marchetto)