Supporting material for MMG 801 Lectures on 'Phylogeny and Comparative Genomics.'
[PDF slides not accessible enough? Please reach out to me]
- Phylogeny & Construction of Phylogenetic Trees (species and gene)
- Comparative Genomics & Pangenomes
- In class hands-on demo for two most useful tools:
- BLAST for similarity searches, MSA (multiple sequence alignment) and phylogenetic trees
- PATRIC for Microbial genomics (esp. as a database)
- For this, please explore the web-versions for the 'how' + papers to orient you on the 'why' & 'what'
- Example input files in the data folder: fasta + saved BLAST search strategy.
- We will address your Qs + use these with the web-tools in class on Thursday!
PDF, video, homework assignment are all accessible w/ your MSU ID Google login.
- Intro to phylogeny
- Evolution of desserts
- Activity: Pizza tree
- Phylogeny and Phylogenetic trees
- Carl Woese and the three domains of life
- Bacterial evolution
- Species trees vs gene trees
- Homologs, Orthologs, Paralogs
- Tangled tree
- Methods to build phylogenetic trees
- Distance-based methods | UPGMA, Neighbor-joining
- Character-based methods | Max. parismony, Max. Likelihood, Bootstrap confidence estimation
- Strengths and Weaknesses of each approach
- Qn: Which alignment is better?
- Sequence evolution & sequence alignment
- The amazing Margaret Dayhoff
- BLOCKS db and BLOSUM substition matrix
- Activity: How do you cluster these? Distance -> Clusters -> Trees
- Qn: Vertical distance in hierarchical rooted trees
- Gene trees & sequence alignment (w/ BLAST)
- NCBI Protein
- NCBI BLAST
- Protein of interest -> [Accession Number -> Fasta sequence] -> BLAST for homologs
- Demonstration of paralogs vs orthologs w/ Ravi 2018 actinobacterial PspA tree
- Tools to explore
- iTol: Interactive Tree of Life
- TimeTree
- NextStrain for CoV, Ebola, Dengue, Mtb and more!
- For similarity searches: BLAST (BLASTp, DELTA-BLAST)
- For multiple sequence alignment: MUSCLE, T-Coffee, Jalview
- For tree building: FigTree, FastTree
- For phylgoenetic trees using distance-based and character-based methods: BEAST, MEGA
- Suggested reading:
- Review on Phylogenetic Methods | a good overview of the phylogenetic tree-building techniques | Molecular phylogenetics: principles and practice. Yang Z, Rannala B. Nat Rev Genet. 2012;13(5):303-314.
- BLAST Original paper | harder to read | Basic local alignment search tool. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. J Mol Biol. 1990 Oct 5;215(3):403-10.
- BLAST | easier to read paper | Steps Used by the BLAST Algorithm. Mount DW. CSH Protoc. 2007 Jul 1;2007:pdb.ip41. doi: 10.1101/pdb.ip41.
- Wiki: BLAST (biotechnology)
- The book, Tangled Tree by David Quammen
- Species trees
- Genome sequencing
- Genome assembly
- Whole genome alignment
- Comparative genomics
- Pangenomes
- PATRIC
- MSU Microsoft Teams (direct message to: Janani Ravi)
- 2020 Office hours (202009) at 4p on Friday (Sep 11) and Tuesday (Sep 16)
- 2021 Office hours: Friday 1–2p; Monday 10–11a