Outline Review of biological fundamentals Genetics example Biological databases/NCBI resources Simplified sequence analysis- where to start Simple sequence comparisons Definitions of related sequences Concepts and types of alignments-the good the bad, and the ugly Dot matrix alignments Computational efficiency Recursion and dynamic programming Substitution matrices: PAM. bloSUM, GonnetOutline • Review of biological fundamentals • Genetics example • Biological databases/NCBI resources • Simplified sequence analysis – where to start… • Simple sequence comparisons • Definitions of related sequences • Concepts and types of alignments – the good, the bad, and the ugly • Dot matrix alignments • Computational efficiency • Recursion and dynamic programming • Substitution matrices: PAM, BLOSUM, Gonnet