Outline Multiple Sequence Alignment -Carillo Lipman Clustal(W Position-Specific Scoring Matrices(PSSM) Information content, Shannon entropy Sequence logos Hidden markov models Other approaches: Genetic algorithms expectation maximization MEME, Gibbs sampler FASTA, Blast searching, Smith-Waterman ·Psi- Blast Reading- Mount p.139-150,152157,161-171,185-198Outline • Multiple Sequence Alignment - Carillo & Lipman, Clustal(W) • Position-Specific Scoring Matrices (PSSM) • Information content, Shannon entropy • Sequence logos • Hidden Markov Models • …Other approaches: Genetic algorithms, expectation maximization, MEME,Gibbs sampler • FASTA, Blast searching, Smith-Waterman • Psi-Blast Reading - Mount p. 139-150, 152-157, 161-171, 185-198