3421 - Fall 2017
Introduction to Molecular Evolution and Bioinformatics
J. Peter Gogarten (OFFICE: BP room 404, firstname.lastname@example.org)
Teaching Assistant: Matthew Fullmer, MATTHEW.FULLMER@uconn.edu
The class meets
MW 11.15AM - 12.05AM AND
Fridays 10.10.AM-11.40AM or 1.25PM-2.55PM
and Wednesday's classes meet in the Phillip E Austin Building (Room 445)
classes will meet in the computer lab located in the Whetton Graduate Center (Room 300A).
(for directions see follow the above links to the UConn campus map)
Reading materials will be posted on huskyCT
-- if you cannot get access, send your netID to email@example.com
There also will be a discussion board on huskyCT. Contributions on the discussion board will count towards your participation grade.
REFRESH THIS PAGE EVERY TIME YOU VISIT
Possibilities to boost your grade:
- Email questions (multiple choice preferred) that could be used for the exams! (counts towards participation).
Essay Assignment (can take the place of one take-home exam).
Exam Questions for Self Study:
Exams #1: Questions with answers
Exam #3: Questions with answers
Exam #4: Questions with answers
Exam #5: Questions with answers
Exam #6: Questions with answers
Exam #7: Questions with answers
Exam# 8: Questions with answers
Additional questions to study for the final (with answers, ASCI drawings are screwed up, if you don't see the answers,
you might need to download the file and open it in acrobat reader )
List of Goals for each class - check them out - discuss if things are not clear.
Midterm, tentative Date: Wednesday October 11th, Austin 445
11/23-11/27 Thanksgiving break
Final: Wednesday, Dec. 13th, 6pm-8pm AUST445
Friday, Dec. 8 last Day of classes
(Please let me know ahead of time, if you have a conflict for this time. See syllabus for exam policy.)
Red: meets in the Computer Lab in the Whetten Graduate Center (300A)
Blue: meets in Room Austin 445
01: Overview; topics; textbook; reading materials;
How will grades be calculated?
- Class 02: Is this Bioinformatics? Protein structure and homology; molecular evolution and bioinformatics
- Computer-lab assignment 01: Intro to SPDBV - binding pocket substrate interactions, multiple subunits
- Class 03: Homology, Life, and Evolution (What is Mol. Evol good for? - Aside on Ebola)
- Computer-lab assignment 02: Aligning divergent protein structures
- Class 4: Ancient paralogs; What is mol. evol. good for?
- Class 5: Sequence divergence, selection, and among site rate variation; Inteins - molecular parasites
- Computer-lab assignment 03: Inteins in SPDBV, splicing and homingendonuclease domain, interactions with DNA
- Class 6: Exam question, Darwinian Evolution, Life
- Class 7: Kropotkin vs Darwin --- Overview on Databanks
- Computer-lab assignment 04: Databank searches, Part A
- Class 8: E- and P-values, fishing expeditions, and the decay of significance
- Class 9: Tree versus Coral of Life - Blast searches
- Computer-lab assignment 05: BLAST and FASTA searches part I
- Class 10: substitution matrices, history of genbank and NCBI
- Class 11: phylogeny and the coral of life, gene plots and within genome recombination
- Computer-lab assignment 06: BLAST searches form the command line
- Class 12: Review session
- Midterm: 11.15 in Austin 445
- ASM Regional meeting, session on Microbial Evolution & Pathogenicity in the Rome Commons Ballroom 9am -12.15
- Class 13: Return midterm, Fate of dublicated genes, simple script to process data
- Class 14: Within genome recombination / Cladistics
- Computer-lab assignment 07: Gene Plots using BLAST searches form the command line
- Class 15: Sequence alignment.
- Class 16: Introns late or early? Functions of introns
- Computer-lab assignment 08: Dotlet and (possibly) PCA of sequence space.
- Class 17: Trees, Topologies and terminology
- Class 18: How to calculate tree from sequnce data, support values
- Computer-lab assignment 09: Alignmnets and trees in seaview.
- Class 19: Phylogenetic reconstruction - approaches, support values, parameters
- Class 20: Why might gene trees differ from one another and from the species phylogney?
- Computer-lab assignment 10: Building phylogenetic trees, missing data and Long Branch Attraction
- Class 21: population genetics, types of selection, role of HGT in evolution,
- Class 22: dN/dS and the hypothesis of neutral evolution
- Computer-lab assignment 11: Building phylogenetic trees, mLRT, MrBayes
- Class 23: dN/dS, purifying selection, GTAs
- Class 24: PSI Blast / the creative powers of HGT
- Computer-lab assignment 12: PSI-Blast
- Class 25: Gene transfer, supertrees and trees from concatenation, constructive neutral evolution
- Class 26: Review session slides
- Computer-lab assignment 14: EMBOSS and dN/dS
- Final: Wednesday, Dec. 13th, 6pm-8pm AUST445
Topics - If you have suggestion for additional topics, please let me know,
Syllabus <- (see for grade calculation, exam policy, and penalties for academic misconduct)
Academic misconduct includes, but is not limited to:
* Providing or receiving assistance on academic work (papers, projects, examinations) in a way that was not authorized by the instructor
* Any attempt to improperly influence (bribery, threats) any member of the faculty, staff, or administration of the University in any matter relating to academics or research
* Doing academic work for another student
* Presenting the same or substantially the same papers or projects in two or more courses without the explicit permission of the instructors
* Situations where one student knowingly assists another student in committing an act of academic misconduct, and any student doing so will be held equally accountable for the violation
For more information see the Community Standards at http://community.uconn.edu/
year's course web page
Send an Email to Peter Gogarten