| Lecture | Date | Topics | Reading* | HW** | Due*** |
| 1 | Jan 21 T |
- Introduction to bioinformatics
(handout)
|
(Introduction to Bioinformatics by Xiong; available on Canvas) |
Survey |
Jan 24 |
| 2 | Jan 23 R |
- Introduction to internet resources: databases and web tools
(handout)
|
(Ch3)
NCBI Help
PubMed Help
Entrez Help |
1 |
Jan 30 |
| 3 | Jan 28 T |
- Fundamentals of Molecular Evolution
(handout)
|
Ch4:pp71-76
Ch7:pp238-248
Molecular Evolution Reading (available on Canvas) |
|
|
| 4 | Jan 30 R |
- Molecular Evolution, Part 2
(handout)
|
2 |
Feb 6 |
| 5 | Feb 4 T |
- Molecular Evolution, Part 3
(handout)
|
|
|
| 6 | Feb 6 R |
- Pairwise alignment (dotplot, dynamic programming algorithm)
(handout)
|
Ch4:pp77-89
Ch5:pp126-139 |
3 |
Feb 9 |
| 7 | Feb 11 T |
- Pairwise alignment (more dynamic programming algorithm, local alignment)
(handout)
|
G1 |
Mar 9 |
| 8 | Feb 13 R |
- Pairwise alignment (gap penalty function)
- Introduction to substitution matrices
(handout)
|
Ch5:pp115-126 |
4 |
Feb 20
|
| 9 | Feb 18 T |
- Amino acid substitution matrices (PAM & BLOSUM)
(handout)
|
| |
| 10 | Feb 20 R |
- Amino acid substitution matrices (Information theory)
- Statistical significance of alignment scores
(handout)
|
Ch5:pp153-155 | 5 |
Feb 27 |
| 11 | Feb 25 T |
- Statistical significance of alignment scores
- Similarity search
(handout)
|
Ch4:pp93-103
Ch5:pp139-152
NCBI BLAST Help
NCBI BLAST Statistics | |
|
| 12 | Feb 27 R |
- Similarity search (FASTA, BLAST)
(handout)
|
6 |
Mar 6 |
| 13 | Mar 4 T |
- Similarity search (BLAST & FASTA statistics)
(handout)
|
| |
| 14 | Mar 6 R |
- Similarity search (BLAST & FASTA statistics)
- Multiple Alignment - Part 1 (Introduction, Clustal W)
(handout)
|
Ch4:pp90-93
Ch6:196-211 |
7 |
Mar 13 |
| 15 | Mar 11 T |
- Multiple Alignment - Part 2 (T-Coffee, MAFFT, etc.)
(handout)
|
Ch4:pp90-93
Ch6:196-211 |
|
|
| 16 | Mar 13 R |
- Multiple Alignment - Part 3 (ClustalO, PRANK, etc.)
- Alignment filtering and benchmarking
(handout)
|
Ch4:pp103-113
Ch6:pp165-178, 211-220 |
8 |
Apr 3 |
| Mar 17 - 21 |
Spring break |
|
|
| 17 | Mar 25 T |
- Domain, motif, profile
- PSI-BLAST
(handout)
|
|
|
|
| 18 | Mar 27 R |
- Hidden Markov models
- Profile hidden Markov models
- Protein family/domain databases (InterPro, etc.)
(handout)
|
Ch6:pp179-196 |
G2 |
May 11 |
19 | Apr 1 T |
- 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
| |
|
| 20 | Apr 3 R |
- Distance estimation (assumptions, gamma distances, synonymous and nonsynonymous substitutions)
- Phylogenetic methods - Introduction
(handout)
|
9 |
Apr 10 |
| 21 | Apr 8 T |
- Phylogenetic methods - Rooting, Distance based (UPGMA, FM, ME, NJ)
(handout)
|
Ch7:pp223-235, 248-251
Ch8:pp276-313
| | |
| 22 | Apr 10 R |
- Phylogenetic methods (Character based: MP and ML)
- Tree searching (Exhaustive, branch-and-bound)
(handout)
|
10 |
Apr 17 |
| 23 | Apr 15 T |
- Tree searching (Heuristic)
- Bootstrap analysis
(handout)
|
| |
| 24 | Apr 17 R |
- Phylogenetic methods/programs (PhyML, etc.)
- Visualization of phylogeny
(handout)
|
(11) optional |
May 1 |
| 25 | Apr 22 T |
- Protein structure databases (PDB, SCOP, CATH)
- Protein secondary structure prediction
(handout)
|
(Ch2)
Ch14:pp567-580
Ch11, Ch12 |
|
|
| 26 | Apr 24 R |
- Protein secondary structure prediction
- Transmembrane region prediction
(handout)
|
12 |
May 11 |
| 27 | Apr 29 T |
- Protein structure prediction (strategies)
- Protein structure prediction (Phyre2, etc.)
(handout)
|
(Ch13:pp529-537) |
|
|
| 28 | May 1 R |
- Protein structure prediction (AlphaFold, etc.)
- Gene prediction methods (simple methods)
(handout)
|
Ch9
Ch10 |
|
|
| 29 | May 6 T |
- Gene prediction methods (simple methods, ab initio methods, etc.)
(handout)
|
|
|
| 30 | May 8 R |
- Gene prediction, genome annotation, etc.
(handout)
|
|
|
| May 12 - May 16 |
Final week |
|
|