MCB 3421 - Fall 2015

Introduction to Molecular Evolution and Bioinformatics

OLD WEBPAGE -- Go back to gogarten.uconn.edu to select current page for theis course!

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

   Teaching Assistant: Amanda Dick (amanda.dick@uconn.edu)

   The class meets
        MW 11.15AM - 12.05AM    AND     Fridays 10.10.AM-11.40AM or 1.25PM-2.55PM
        Monday's and Wednesday's classes meet in Gentry 119E
        Friday's classes will meet in the computer lab located on the ground floor of the Chemistry building (T115).

(for directions see here, search for CHM or GENT)    

   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 quizzes or exams! (counts towards participation).

Optional Essay Assignment (can take the place of one take-home exam).

Take Home Exams: #1 (doc/pdf/answ), #2 (doc/pdf/answ), #3 (doc/pdf/answ), #4 (doc/pdf/answ), #5 (doc/pdf/answ), #6 (doc/pdf/ans), #7 (doc/pdf/ans), #8 (doc/pdf/ans), #9 (doc/pdf/ans), #10 (ans)
Midterm with some answers

IMPORTANT DATES:
      Midterm: (preliminary) Wednesday, Oct. 14, 11.10AM- 12.05PM
       Final: (preliminary) Wednesday, Dec. 16, 10.30am - 12.30pm
       11/23-11/27 Thanksgiving break
       Friday,  Dec. 11 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 Chemistry Building (ground floor, T115)
   Blue: meets in Room Gentry 119E

• Class 01: Overview; topics; textbook; reading materials; How will grades be calculated?
• Class 02: Homology, similarity, function
• Comp. Lab 01: Intro to SPDBV
• Class 03: Homology, Life, and Evolution (What is Mol. Evol good for? - Aside on Ebola)
• Comp. Lab 02: Aligning protein structures in SPDBV
• Class 04: Origin of life and evolution
• Class 05: Evolution by natural selection (and other mechanisms), JC model
• Comp. Lab 03: Inteins in SPDBV, splicing and homonuclease domain, interactions with DNA
• Class 6: Natural Selection, Mutual aid, Mutationism, Modern synthesis
• Class 7: Tree or Web of Life? Databanks at NCBI
• Comp. Lab 04: Databases at the NCBI, Entrez and others
• Class 8: Exponential curves and errors in databank
• Class 9: How to access significant similarity in comparing sequences
• Comp. Lab 05: Statistics of sequence comparison
• Class 10: Blast searches and E-values
• Class 11: Comparing genomes using blast I
• Comp. Lab 06: Commandline Blast
• Class 12: Review session / finish items from class 11
• Midterm
• Comp. Lab 07: Commandline Blast continued -> gene plot
• Class 13: Gene plot and strand bias
• Class 14: Sequence space / cladistics part I
• Comp. Lab 08: Sequence alignment I
• Class 15: cladistics part II / introns late or early
• Class 16: sequence alignment
• Comp. Lab 09: Multiple sequence alignment
• Class 17: Phylogenetic reconstruction I
• Class 18: Phylogenetic reconstruction II
• Comp. Lab 10: phylogenetic trees I
• Class 19: How to interpret trees
• Class 20: Population genetics, genetic drift and selection
• Comp. Lab 11: LBA and other artifacts
• Class 21: Population genetics, types of selection
• Class 22: Detecting types of selection
• Comp. Lab 12: MrBayes and dN/dS
• Class 23: Selective Sweeps and HGT
• Class 24: Neutral pathways to complexity
• Comp. Lab 13: PSI Blast
• Class 25: PSI blast, discussion HGT in water-bear example
• Class 26: supertree vs supermatrix - review session
• Comp. Lab 14: Taxplot, Emboss, Mummer

Final Prep: Listing of goals and slides as pdfs

• Final: Wednesday, Dec. 16, 10.30am - 12.30pm
  

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