1. CISC 667 Intro to Bioinformatics (Spring 2007) Review session for Mid-Term
CISC667, S07, Lec14, Liao

2. About the mid-term closed-book Three parts
Basic molecular biology [20 points]
Sequence alignments [45 points]
Hidden Markov models [35 points]
CISC667, S07, Lec14, Liao

3. Basics of Molecular biology
Central dogma
Transcription
Translation
Genetic code
DNA
Double helix
Watson-crick binding
Genes
Compositional Structure
Reading frames
Proteins
Genome sequencing (Sanger method)
CISC667, S07, Lec14, Liao

4. Sequence alignments Motivations Concepts and assumptions
Substitution scores
Position independence …
Dynamic programming
Problems can be dissect to sub-problems
Recurrence equations
DP Table
Traceback
Global v.s. local alignments
Pairwise v.s. multiple alignments
Progressive approaches
Score statistics: E-value, p-value.
CISC667, S07, Lec14, Liao

5. Hidden Markov models Motivations Concepts and assumptions Three tasks
Decoding (Viterbi algorithm)
Recurrence
Dynamic programming
Model likelihood (Forward algorithm, Backword algorithm)
Model building
Labeled data
Unlabeled data (Viterbi training)
CISC667, S07, Lec14, Liao