| Lecture | Date | Topics | Reading* | HW** | Due*** |
| 1 | Jan 23 T |
- Introduction to bioinformatics
(handout)
|
(Introduction to Bioinformatics by Xiong; available on Canvas) |
Survey |
Jan 26 |
| 2 | Jan 25 R |
- Introduction to internet resources: databases and web tools
(handout)
|
(Ch3)
NCBI Help
PubMed Help
Entrez Help |
1 |
Feb 1 |
| 3 | Jan 30 T |
- Fundamentals of Molecular Evolution
(handout)
|
Ch4:pp71-76
Ch7:pp238-248
Molecular Evolution Reading (available on Canvas) |
|
|
| 4 | Feb 1 R |
- Molecular Evolution, Part 2
(handout)
|
2 |
Feb 8 |
| 5 | Feb 6 T |
- Molecular Evolution, Part 3
(handout)
|
|
|
| 6 | Feb 8 R |
- Pairwise alignment (dotplot, dynamic programming algorithm)
(handout)
|
Ch4:pp77-89
Ch5:pp126-139 |
3 |
Feb 11 |
| 7 | Feb 13 T |
- Pairwise alignment (more dynamic programming algorithm, local alignment)
(handout)
|
G1 |
Mar 11 |
| 8 | Feb 15 R |
- Pairwise alignment (gap penalty function)
- Introduction to substitution matrices
(handout)
|
Ch5:pp115-126 |
4 |
Feb 22
|
| 9 | Feb 20 T |
- Amino acid substitution matrices (PAM & BLOSUM)
(handout)
|
| |
| 10 | Feb 22 R |
- Amino acid substitution matrices (Information theory)
- Statistical significance of alignment scores
(handout)
|
Ch5:pp153-155 | 5 |
Feb 29 |
| 11 | Feb 27 T |
- Statistical significance of alignment scores
- Similarity search
(handout)
|
Ch4:pp93-103
Ch5:pp139-152
NCBI BLAST Help
NCBI BLAST Statistics | |
|
| 12 | Feb 29 R |
- Similarity search (FASTA, BLAST)
(handout)
|
6 |
Mar 7 |
| 13 | Mar 5 T |
- Similarity search (BLAST & FASTA statistics)
(handout)
|
| |
| 14 | Mar 7 R |
- Similarity search (BLAST & FASTA statistics)
- Multiple Alignment - Part 1 (Introduction, Clustal W)
(handout)
|
Ch4:pp90-93
Ch6:196-211 |
7 |
Mar 21 |
| Mar 10 - 17 |
Spring break |
|
|
| 15 | Mar 19 T |
- Multiple Alignment - Part 2 (T-Coffee, MAFFT, etc.)
(handout)
|
Ch4:pp90-93
Ch6:196-211 |
G2 |
May 14 |
| 16 | Mar 21 R |
- Multiple Alignment - Part 3 (filtering, benchmarking)
- Domain, motif, profile
(handout)
|
Ch4:pp103-113
Ch6:pp165-178, 211-220 |
|
|
| 17 | Mar 26 T |
- Multiple Alignment - Part 4 (benchmarking)
- Domain, motif, profile
- PSI-BLAST
(handout)
|
8 |
Apr 4 |
| 18 | Mar 28 R |
- Hidden Markov models
- Profile hidden Markov models
(handout)
|
Ch6:pp179-196 |
|
|
19 | Apr 2 T |
- Protein family/domain databases (InterPro, etc.)
- Distance estimation - nucleotide sequences
(handout)
|
Ch7:pp235-238, 251-255
Ch8:pp267-276
| |
|
| 20 | Apr 4 R |
- Distance estimation (nucleotide and amino acid sequences)
(handout)
|
9 |
Apr 11 |
| 21 | Apr 9 T |
- Distance estimation (synonymous and nonsynonymous substitutions)
- Phylogenetic methods - Introduction, Distance based (UPGMA)
(handout)
|
Ch7:pp223-235, 248-251
Ch8:pp276-313
| | |
| 22 | Apr 11 R |
- Phylogenetic methods (Distance based: FM, ME, NJ, Character based: MP)
(handout)
|
10 |
Apr 23 |
| 23 | Apr 16 T |
- Phylogenetic methods (Character based: ML)
- Tree search
- Bootstrap analysis
(handout)
|
| |
| 24 | Apr 18 R |
- Phylogenetic methods/programs (PhyML, etc.)
- Visualization of phylogeny
(handout)
|
(11) optional |
May 5 |
| 25 | Apr 23 T |
- Protein structure databases (PDB, SCOP, CATH)
- Protein secondary structure prediction
(handout)
|
(Ch2)
Ch14:pp567-580
Ch11, Ch12 |
|
|
| 26 | Apr 25 R |
- Protein secondary structure prediction
- Transmembrane region prediction
(handout)
|
12 |
May 12 |
| 27 | Apr 30 T |
- Transmembrane region prediction
- Protein structure prediction (strategies)
(handout)
|
(Ch13:pp529-537) |
|
|
| 28 | May 2 R |
- Protein structure prediction (FUGUE, Phyre2, etc.)
- Gene prediction methods (simple methods)
(handout)
|
Ch9
Ch10 |
|
|
| 29 | May 7 T |
- Gene prediction methods (similarity methods, ab initio methods, GENSCAN, etc.)
(handout)
|
|
|
| 30 | May 9 R |
- Gene prediction, genome annotation, etc.
(handout)
|
|
|
| May 13 - May 17 |
Final week |
|
|