A C G T A T G G T T A AC T A G T T A G G A A T C G C G C A T T A T G T C C A C G T T A G G T T G A A C G G C A G G T T T A A A T C G A T T C.

Presentazione sul tema: "A C G T A T G G T T A AC T A G T T A G G A A T C G C G C A T T A T G T C C A C G T T A G G T T G A A C G G C A G G T T T A A A T C G A T T C."— Transcript della presentazione:

1

2 A C G T A T G G T T A AC T A G T T A G G A A T C G C G C A T T A T G T C C A C G T T A G G T T G A A C G G C A G G T T T A A A T C G A T T C C A C G T T A T G A A A T T G G G G C A G G T T T A A C G C G C C C

3 M V N S T P L K G Q Metionina Valina Asparagina STOP Serina Treonina
A U G G UU A A C U A G UU A G G A A U C G C G C A U U A U G U C C A C G U Metionina Valina Asparagina STOP Serina Treonina Prolina Lisina Leucina Glicina Glutamina A C G U U A G G U U G A A C G G C A G G U U U A A A U C G A U U C C C A G U A C G U U A UG A A A U U G G G G C A G G U U U A A C G C G C C C

4 ATTACGGCCATGCGGAGCCGGAAG
presente in ? algoritmo che richiede un numero di confronti pari alla lunghezza di

5 confronto approssimato di stringhe
ALLINEAMENTO T G T A C G G A A T C G G A T C T C C G A C C A T C G G A 4 3 + = 7 T G - T A - C G G A A T C G G A T - C T - C C G - A C C A T C G G A T G C TAC C G G A C C A T C G G A

6 T G T A C G G A A T C G G A T C G A T C G A T G T A C G G A A T C G G A

7 4 3 + = 7 T - G T A C - G G A A T C G G A T C - T - C C - G A C C A T C G G A T G - T A - C G G A A T C G G A T - C T - C C G - A C C A T C G G A

8 cammino minimo quante operazioni ? N.B. : il numero di cammini è molto elevato impossibile la valutazione esplicita !

9 RICORSIONE ! +1 = min +1

10 ogni arco viene considerato esattamente una volta
numero operazioni = numero archi = due sequenze di 1000 basi richiedono un milione di operazioni

11 Diverso modello: sostituzioni ammesse
T G T A C G G A A T C G G A T C T C C G A C C A T C G G A 4 T G T A C G G A A T C G G A T C T C C G - A C C A T C G G A 2 2 8

12 T G T A C G G A A T C G G A T C G A 6 14

13 T G T A C G G A - A T C G G A T C T C C G A C C A T C G G A T G T A C G G A A T C G G A T C T C C G - A C C A T C G G A

14

15 ALLINEAMENTO MULTIPLO
T G T A C G G A A T C G G A T C T C C G A C C A T C G G A A C T C A G A C A A T G A T G T A C G - G A A T C G G A T C T C C G A C C A T C G G A A C T C A G A C A A T G A

16

17 Numero confronti = prodotto lunghezze stringhe
3 stringhe lunghe 1000 un miliardo di operazioni !

18 ? ATAGA CTAGA CTAGA ATGA CTGA AGGA ATGA TAGA CTGA ATGA TAGA TACA TAGA A G - G A - T A C A - T A G A C T - G A A T - G A A G - G A - T A C A - T A G A C T - G A A T - G A

19 AUGCCGAUUCAACGGUCCUACUCGGACUUUACC
M P I Q R S Y S D F T M R I S R S D S D Y T punteggio (M<->M, P<-> R ...) basato sulle probabilità di mutazione

20 RICOSTRUZIONE DEI FRAMMENTI

21 ACGTTACG TTACGGAT CGGATTCA CGGCGATT AACAAGCTT CGGAATCG TTACCGGAT CGGTTAGG CGAATTAG TGGCGAA GGCCTTAA ACGACGAT GCATTCGA ATATCGAT CGCGCGAA TGTGCATA ACCGGAC TGTCGCGA CGCGCGAT GTGTAGAG CTTGATCT CGGATATA CGCGATAT TGTGAATA ACGTTACG TTACGAAT CGGATTCA CGGCGATT AACCAGCTT CGGAATCG TTACCGGAT CGGTTAGG CGAATTAG TGGCGAA AGCCTTAA ACGACGAT GCATTCGA ATATCGAT CGCGCGAA TGTGCATA ACCGGAC TGTCGCGA CGCGCGAT GTGCAGAG CTTGATCT CGGATATA CGCGATAT TGTGAATA ACGTTACG TTACGGAT CGGATTTA CGGCGATT AACAAGCTT CGGAATCG TTACCGGAT CGGTTAGG AGAATTAG TGGCGAA GGCCTTAA ACGACGAT GCATTCGA ATATCGAT CGCGCGAA TGTGCATA ACCGGAC TCTCGCGA CGCGCGAT GTGTAGAG CTTGATCT CGGATATA CGCGCTAT TGTGAATA ACATTACG TTACGGAT CGGATTCA CGGCGACT AACAAGCTT CGGAATCG TTACCGGAT CGGTTAAG CGAATTAG TGGCGAA GGCCTTAA ACGACGTT GCATTCGA ATATCGAT CGCGCGAA TGTGCATA ACCGGAC TGTCGCGA CGCGCGAT TTGTAGAG CTTGATCT CGGATATA CGCAATAT TGTGAATA ACGTTACG TTACTGAT CGGATTCA CGGCGATT AACAAGCGT CGGAATCG TTACCGGAT CGGTTAGG AGAATTAG TGGCGAA GGCCTTAA ACGACGAT GCATTGGA ATATCGAT CGCGCGAA TGTGCATA AACGGAC TGTCGCGA CGCGCGAT GTGTAGAG CTTGTTCT CGGATATA CGCGATAT TGTGAATA ACGTTACG TTACGGAT CGGATTCA CGGCAATT AACAAGCTT CGGAATAG TTACCGGAT CGGTTAGG CGAATTAG TGGCGAA GGCCTTAA ACGACGAT GTATTCGA ATATCGAT CGCGCGAA TGTGCATA ACCGGAC TGTCGCGA CGCTCGAT GTGTAGAG CTTGATCT AGGATATA CGCGATAT TGTGAATA

22 ACGTTACG TTACGGAT CGGATTCA CGGCGATT AACAAGCTT CGGAATCG TTACCGGAT CGGTTAGG CGAATTAG TGGCGAA GGCCTTAA ACGACGAT GCATTCGA ATATCGAT CGCGCGAA TGTGCATA ACCGGAC TGTCGCGA CGCGCGAT GTGTAGAG CTTGATCT CGGATATA CGCGATAT TGTGAATA ACGTTACG TTACGAAT CGGATTCA CGGCGATT AACCAGCTT CGGAATCG TTACCGGAT CGGTTAGG CGAATTAG TGGCGAA AGCCTTAA ACGACGAT GCATTCGA ATATCGAT CGCGCGAA TGTGCATA ACCGGAC TGTCGCGA CGCGCGAT GTGCAGAG CTTGATCT CGGATATA CGCGATAT TGTGAATA ACGTTACG TTACGGAT CGGATTTA CGGCGATT AACAAGCTT CGGAATCG TTACCGGAT CGGTTAGG AGAATTAG TGGCGAA GGCCTTAA ACGACGAT GCATTCGA ATATCGAT CGCGCGAA TGTGCATA ACCGGAC TCTCGCGA CGCGCGAT GTGTAGAG CTTGATCT CGGATATA CGCGCTAT TGTGAATA ACATTACG TTACGGAT CGGATTCA CGGCGACT AACAAGCTT CGGAATCG TTACCGGAT CGGTTAAG CGAATTAG TGGCGAA GGCCTTAA ACGACGTT GCATTCGA ATATCGAT CGCGCGAA TGTGCATA ACCGGAC TGTCGCGA CGCGCGAT TTGTAGAG CTTGATCT CGGATATA CGCAATAT TGTGAATA ACGTTACG TTACTGAT CGGATTCA CGGCGATT AACAAGCGT CGGAATCG TTACCGGAT CGGTTAGG AGAATTAG TGGCGAA GGCCTTAA ACGACGAT GCATTGGA ATATCGAT CGCGCGAA TGTGCATA AACGGAC TGTCGCGA CGCGCGAT GTGTAGAG CTTGTTCT CGGATATA CGCGATAT TGTGAATA ACGTTACG TTACGGAT CGGATTCA CGGCAATT AACAAGCTT CGGAATAG TTACCGGAT CGGTTAGG CGAATTAG TGGCGAA GGCCTTAA ACGACGAT GTATTCGA ATATCGAT CGCGCGAA TGTGCATA ACCGGAC TGTCGCGA CGCTCGAT GTGTAGAG CTTGATCT AGGATATA CGCGATAT TGTGAATA

23 ACCGT CGTGC TTAC TACCGT - - ACCGT - - CGTGC TTAC - TACCGT - - TTACCGTGC TTAC - TACCGT - - - - ACCGT - - CGTGC 1 + 2 = ___ 4

24 TAGG AGGT CGTC GTCG TAGG AGGT 1 TAGG AGGT 3 TAGG AGGT CGTC GTCG 4 1 3 4 4 2 1 2 4

25 TAGG 4 1 3 4 4 GTCG AGGT 2 1 4 2 4 4 CGTC CGTC - GTCG TAGG - AGGT CGTCGTAGGT lunghezza 10

26 TAGG 1 4 4 3 4 4 GTCG AGGT 2 TAGG 1 4 2 4 - AGGT 4 - - GTCG CGTC - - CGTC TAGGTCGTC lunghezza 9 CGTCGTAGGT

27 ALBERI FILOGENETICI A B C D E F

28 a b c d e A 1 B C D E F

29 00110 00010 00100 10010 00011 00101 00100 01011 00010 10011 10010

30 1 1 1 1

31 1 1 1 1

32 1 1 1 1

33 a b c d e A 1 B C D E F esiste un albero filogenetico perfetto con A,B,C,D,E,F nodi?

34 2 foglie A B A B C 3 foglie A B C 4 foglie 12 6 18 5 foglie 60 30 120

35 caratteri ordinati: solo 0 --> 1 ammesso
problema facile a b c d e A B C D E F 1

36 a b c d e A 1 B C D E F

37 A B C D E F a b c d e 1 a b c d e E C 1 B F D A a b c d e C F B E A D

38 caratteri non ordinati (filogenia perfetta)
B C D E F a b c d e 1 f g A B C D E F a b c d e 1 f g

39 E B C F D A