Algorithms on Sequences

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Needleman & Wunsh’s algorithm (2) X = a c t Y = a g t optimal a c alignment a g + substitution (t,t) optimal a c t alignment a g t MAX optimal a c t alignment a g + substitution (t,-) optimal a c alignment a g t + substitution (-,t) Needleman & Wunsh’s algorithm (3) act agt act ag act a ac agt ac ag ac a a agt a ag a a
Needleman & Wunsh’s algorithm (4) • The score S N,M is calculated from the recurrence equation : S I,J-1 - Gap S I,J = Max S I-1,J-1 + Sub (X I ,Y J ) S I-1,J - Gap Needleman & Wunsh’s algorithm (5) T A G A C T T A G C T A i,j S I,J-1 - Gap S I,J = Max S I-1,J-1 + Sub (XI ,YJ ) S I-1,J - Gap Complexity : filling a matrix of size N x M Result : S N,M
Page 1 and 2: Bioinformatics Algorithms</
Page 3 and 4: Alignment of two sequences • Matc
Page 5: DP applied to alignments • Given
Page 9 and 10: Smith & Waterman algorithm (1) •
Page 11 and 12: E I,J = MAX Gotoh’s algorithm (2)
Page 13 and 14: Identity and default Blast Matrices
Page 15 and 16: Other substitution matrices • Phy
Page 17 and 18: Example 1 : easy case ALIGN calcula
Page 19 and 20: Validation of a global alignment (2
Page 21 and 22: PRSS compares a test sequence to a
Page 23 and 24: BLASTN 1.4.7 [16-Oct-94] [Build 17:
Page 25 and 26: Principle of the heuristics (1) 1 -
Page 27 and 28: Tradeoff sensitivity / rapidity W 1
Page 29 and 30: Recent Blasts • Blast2 (Gapped Bl

Algorithms on Sequences

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