MCB 3421 - Fall 2018

Introduction to Molecular Evolution and Bioinformatics

   Instructor: J. Peter Gogarten (OFFICE: BP room 404, gogarten@uconn.edu)

   Teaching Assistant: Yutian “Tian” Feng yutian.feng@uconn.edu

   The class meets
        MW 11.15AM - 12.05PM    AND     Fridays 10.10.AM-11.40AM or 1.25PM-2.55PM
        Monday's and Wednesday's classes meet in Koons Hall (might change) Room 105
        Friday's classes will meet in the computer lab located in the Whetton Graduate Center (Room 300A).

(for directions 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 gogarten@uconn.edu

   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 IT

Possibilities to boost your grade:

• Email questions (multiple choice preferred) that could be used for the exams! (counts towards participation).
• Optional Essay Assignment (can take the place of one take-home exam).

Exam Questions for Self Study:

Takehome Exam #1, #2, #3, #4, Additional Questions for Midterm, #5, #6, #7, #8 , Additional questions for final (with answers)

List of Goals and Link to study materials for each class - check them out - discuss if things are not clear.

IMPORTANT DATES:
      Midterm, Date: Wednesday October 17th, Koons 105 at 11.15am
        11/19-11/23 Thanksgiving break 
       Final: Wednesday Dec. 12, 6-8PM Koons 105
       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 Koons Hall (105)

• Class 01: Overview; topics; textbook; reading materials; How will grades be calculated?
• Class02: The concept of homology, convergent evolution, secondary structure elements in proteins
• Computer-lab assignment 01: Intro to chimera - binding pocket substrate interactions
• Class03: The RNA world hypothesis, ancient gene duplications
• Computer-lab assignment 02: Comparing structures for ancient duplicated genes / following a structure through the catalytic cycle
• Class04: Convergent evolution, the power of selection, life and genetic material
• Class05: Sequence divergence, inteins, life and genetic material
• Computer-lab assignment 03: Indentifying domains in multidomain proteins (example inteins) / optional aligning histones and poteasome subunits
• Class06: Natural selection, the tangled tree,
• Class07: Mutual Aid, the modern synthesis, entrez
• Computer-lab assignment 04: Databank searches via Entrez
• Class08: Significance measures, false positives vs false negatives,
• Class09: Bonferroni correction, history of genebank, problems that databanks encounter
• Computer-lab assignment 05: Statistics of sequence comparison
• Class10: Blast searches, the unix command line
• Class 11: Strand bias and recombination
• Computer-lab assignment 06: Database searches using BLAST+ executables
• Class 12: Scripts, Gene Plots, Late heavy bombardment.
• Class 13: Measures for sequence similarities, review of within genome recombination,discussion of new genes from ... (including erection of post mating hybridization barriers),
• Computer-lab assignment 07: Database searches using BLAST+ executables (continued)
• Claas 14: Review for midterm - sequence space
• Midterm
• Computer-lab assignment 08: Dotlet exercises and Jalview PCA.
• October 17th: Midterm
• Class 15: A natural txonomy? Hennig versus Mayr
• Class 16: October 24th: Charles Darwin is visiting
• Computer-lab assignment 09: Analyzing genomic size datasets using simple scripts
• Class 17: Introns Early versus Introns late. Multiple Sequence Alignement (MSA)
• Class 18: Intro to phylogenetic reconstruction
• Computer-lab assignment 10: Trees and alignments in SEAVIEW.
• Class 19: Phylogenetics continued: ml, Bayes, Long Branch Attraction
• Class 20: Long Branch Attraction, causes for phylogenetic conflict
• Computer-lab assignment 11: Long Branch Attraction and Likelihood Ratio Test
• Class 21: Genetic drift and synonymous substitution
• Class 22: Silent site diversity and population size, dN/dS, models to estimate dN/dS using Bayesian approaches.
• Computer-lab assignment 12: MrBayes and dN/dS exercises
• Class 23: Types of selection; Does purifying selection=function beneficial to the organism? GTAs
• Class 24: PSI-Blast, HGT - importance & how to detect it
• Computer-lab assignment 13: PSI-Blast exercises
• Class 25: Super-tree vs super-matrix approaches. how to detect gene transfer events.
• Class 26: Review session for final.
• Computer-lab assignment 14: python, influenza virus, mummer
• Final Wednesday Dec. 12, 6pm

Final Wednesday 6pm in

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
* Plagiarism
* 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/

Send an Email to Peter Gogarten

Go the Gogarten-Lab homepage