BIOS 477/877 Bioinformatics and Molecular Evolution (3 credits)

• Introduction to bioinformatics (handout)

( Introduction to Bioinformatics by Xiong; available on Canvas)

• Introduction to internet resources: databases and web tools (handout)

(Ch3)
NCBI Help
PubMed Help
Entrez Help

• Fundamentals of Molecular Evolution (handout)

Ch4:pp71-76
Ch7:pp238-248
Molecular Evolution Reading; available on Canvas

• Molecular Evolution, Part 2 (handout)

• Molecular Evolution, Part 3 (handout)

• Pairwise alignment (dotplot, dynamic programming algorithm)(handout)

Ch4:pp77-89
Ch5:pp126-139

• Pairwise alignment (more dynamic programming algorithm, local alignment) (handout)

• Pairwise alignment (gap penalty function)
• Introduction to substitution matrices (handout)

Ch5:pp115-126

• Amino acid substitution matrices (PAM & BLOSUM) (handout)

• Amino acid substitution matrices (Information theory)
• Statistical significance of alignment scores (handout)

Ch5:pp153-155

• Statistical significance of alignment scores
• Similarity search (handout)

Ch4:pp93-103
Ch5:pp139-152
NCBI BLAST Help
NCBI BLAST Statistics

• Similarity search (FASTA, BLAST) (handout)

• Similarity search (BLAST & FASTA statistics) (handout)

• Similarity search (BLAST & FASTA statistics)
• Multiple Alignment - Part 1 (Introduction, Clustal W) (handout)

Ch4:pp90-93
Ch6:196-211

• Multiple Alignment - Part 2 (T-Coffee, MAFFT, etc.) (handout)

Ch4:pp90-93
Ch6:196-211

• Multiple Alignment - Part 3 (ClustalO, PRANK, etc.)
• Alignment filtering and benchmarking (handout)

Ch4:pp103-113
Ch6:pp165-178, 211-220

• Domain, motif, profile
• PSI-BLAST (handout)

• Hidden Markov models
• Profile hidden Markov models
• Protein family/domain databases (InterPro, etc.) (handout)

Ch6:pp179-196

• Other protein family/domain databases and searches (HHblits, etc.)
• Distance estimation - for nucleotide and protein sequences (handout)

Ch7:pp235-238, 251-255
Ch8:pp267-276

• Distance estimation (assumptions, gamma distances, synonymous and nonsynonymous substitutions)
• Phylogenetic methods - Introduction (handout)

• Phylogenetic methods - Rooting, Distance based (UPGMA, FM, ME, NJ) (handout)

Ch7:pp223-235, 248-251
Ch8:pp276-313

• Phylogenetic methods (Character based: MP and ML)
• Tree searching (Exhaustive, branch-and-bound) (handout)

• Tree searching (Heuristic)
• Bootstrap analysis (handout)

• Phylogenetic methods/programs (PhyML, etc.)
• Visualization of phylogeny (handout)

• Protein structure databases (PDB, SCOP, CATH)
• Protein secondary structure prediction (handout)

(Ch2)
Ch14:pp567-580
Ch11, Ch12

• Protein secondary structure prediction
• Transmembrane region prediction (handout)

• Protein structure prediction (strategies)
• Protein structure prediction (Phyre2, etc.) (handout)

(Ch13:pp529-537)

• Protein structure prediction (AlphaFold, etc.)
• Gene prediction methods (simple methods) (handout)

Ch9
Ch10

• Gene prediction methods (simple methods, ab initio methods, etc.) (handout)

• Gene prediction, genome annotation, etc. (handout)