Sequence Analysis -- Pairwise Global Alignment of Sequences -- Alignment and Evolution -- A Scoring Scheme for the Model -- Finding Highest-Scoring Alignments with Dynamic Programming -- Determine H[subscript i, j] -- Use of matrices -- Finding the alignments that give the highest score -- Gaps -- Scoring Matrices -- Scoring Gaps: Gap Penalties -- Dynamic Programming for General Gap Penalty -- Dynamic Programming for Affine Gap Penalty -- Alignment Score and Sequence Distance -- Pairwise Local Alignment and Database Search -- The Basic Operation: Comparing Two Sequences -- Dot Matrices -- Filtering -- Repeating segments -- Dynamic Programming -- Initialization -- Finding the best local alignments -- Algorithms -- Scoring matrices and gap penalties -- Database Search: BLAST -- The procedure -- Preprocess the query: make the word list -- Scanning the database sequences -- Extending to HSP -- Introducing gaps -- Algorithm -- Statistical Analysis -- Hypothesis Testing for Sequence Homology -- Random generation of sequences -- Use of Z values for estimating the statistical significance -- Statistical Distributions -- Poisson probability distribution -- Extreme value distributions -- Theoretical Analysis of Statistical Significance -- The P value has an extreme value distribution -- Theoretical analysis for database search -- Probability Distributions for Gapped Alignments -- Assessing and Comparing Programs for Database Search -- Sensitivity and specificity -- Discrimination power -- Using more sequences as queries.