About 60% of the final will be over chapters 5, 6, and 7. The remaining 40% will be more comprehensive in nature.

Chapters 5. Character-Based Methods of Phylogenetics

Parsimony, informative sites, weighted vs. unweighted parsimony

Strategies for faster searches: branch-and-bound, heuristic searches,

Consensus trees: strict, 50% majority-rule

Tree Confidence: bootstrap tests

Molecular Phylogenies, tree of life, human origins

Chapter 6. Genomics and Gene Recognition

General characteristics of the prokaryotic genomes: GC content, gene density

Prokaryotic gene structure including: promoter elements, consensus sequence, operon, regulatory proteins (negative regulator and positive regulator), open reading frames, termination sequences,

General characteristics of Eukaryotic gene structure: exons, introns, alternative splicing, gene density

Eukaryotic gene structure including: promoter elements (RNA polymerase I, II, and III), basal transcription factors (TATA-binding protein, TBP), TBP-associated factors (TAFs), initiator sequence, regulatory protein binding sites, constitutive transcription factors, regulatory transcription factors, enhanceosomes, open reading frames

GC content in eukaryotic genomes

CpG islands, methylation

histones, chromatin, euchromatin, heterochromatin

isochores

codon usage bias

gene expression

cDNA, ESTs

Microarray/DNA chip

transposons, retrotransposons

repetitive elements, minisatellites and microsatellites, MITES, LINES, SINES

Chapter 7. Protein and RNA Structure Prediction (general ideas from this chapter)

Amino acids characteristics, polypeptide composition

Secondary structure (phi, psi), Chou-Fasman algorithm

Tertiary and quaternary structure and the forces that drive protein folding (hydrophobicity, disulfide bonds)

Algorithms for modeling protein folding: lattice models, hydrophobic zipper mechanism, off-lattice models, energy functions and optimization

Structure prediction: comparative modeling, threading