Algorithms on Sequences

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Dayhoff’s Matrices (PAM) • M.O. Dayhoff, 1978, Atlas of Protein Sequence and Structure. Initial matrix deduced from the alignment of 71 families of highly homologous proteins (>1000 sequences). • Replacement frequency Matrix of each amino acid X with one of the 19 others (relative frequency for homogeneity reasons) = PAM (Percent Accepted Mutation). • The model of evolution of Dayhoff assumes that proteins have diverged due to the accumulation of random mutations. PAM N is the power N of the matrix, thus simulating an evolution rate. Standard value of N =250 Each value is the probability of substitution of a given aa with another one. The greater the value, the more likely the replacment. 0 is equivalent to a random mutation.
Other substitution matrices • Physico-chemical properties may be used to build score matrices. • Chemical properties • Hydrobobicity • Secondary structures (membrane domains) • Tertiary structures • ...
Page 1 and 2: Bioinformatics Algorithms</
Page 3 and 4: Alignment of two sequences • Matc
Page 5 and 6: DP applied to alignments • Given
Page 7 and 8: Needleman & Wunsh’s algorithm (4)
Page 9 and 10: Smith & Waterman algorithm (1) •
Page 11 and 12: E I,J = MAX Gotoh’s algorithm (2)
Page 13: Identity and default Blast Matrices
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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