MCB 3421 - Fall 2016

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

Introduction to Molecular Evolution and Bioinformatics

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

   Teaching Assistant: Tim Harlow t.harlow@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 140
        Friday's classes will meet in the computer lab located in the Whetton Graduate Center (Room 300A).

(for directions see here, search for WGC 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/ans), #2(doc/pdf/ans), #3(doc/pdf/ans), #4 (doc/pdf/ans), #5(doc/pdf/ans), #6 (doc/pdf/ans). #7(doc/pdf/ans), #8(doc/pdf/ans)

Additional Questions for midterm (doc/pdf/ans)

Additional Questions to prepare for the FINAL

IMPORTANT DATES:
      Midterm: Wednesday October 12th
       Final: Wednesday Dec. 14, 6pm in GENT 140
       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 Whetten Graduate Center (300A)
   Blue: meets in Room Gentry 140

• Class 01: Overview; topics; textbook; reading materials; How will grades be calculated?
• Class 02: Relation between Bioinformatics and Evolution.
• 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: Early evolution of life and evolution through natural selection
• Class 05: Inteins, sequence divergence and selection.
• Comp. Lab 03: Inteins in SPDBV, splicing and homingendonuclease domain, interactions with DNA
• Class 06: Natural selection versus mutual aid
• Class 07: Exponential functions, overview on databanks, problems associated with ownership of records
• Comp. Lab 04: Simple databank searches at the NCBI
• Class 08: Processes acting in the evolution of natural systems, images for evolution, statistics of sequence comparison
• Class 09: Blast searches
• Comp. Lab 05: Intro to the command line and statistics of sequence comparison.
• Class 10: Margaret Dayhoff, substitution matrices, and databank search errors
• Class 11: BLAST, gene-plot, genome rearrangements and strandbias
• Comp. Lab 06: BLAST from the command-line
• Class 12: Review session (Take home exams 2 and 3)
• Midterm: Wednesday, Oct. 12th
• Comp. Lab 07: BLAST from the command-line -> geneplot Comp. lab 07 add on
• Class 13: Discussion gene plots, Cladistics
• Class 14: Cladistics continued - sequence alignment
• Comp. Lab 08: dotlet and jalview exercises
• Class 15: Review cladistics and alignment, Introns Early versus Introns Late
• Class 16: Introns Early versus Introns Late - Introduction to trees
• Comp. Lab 09: multple sequence alignment
• Class 17: Trees and phylogenetic reconstruction
• Class 18: Bacterial Species (slides)
• Comp. Lab 10: multple sequence alignment -> trees
• Class 19: Structure of Bacterial Population (slides)
• Class 20: Gene tree versus species tree. LBA
• Comp. Lab 11: phylogenetic reconstruction and Long Brach Attraction
• Class 21: Neutral evolution, genetic drift versus selection
• Class 22: Genetic drift and selection, HGT and evolution
• Comp. Lab 12: testing models using the MLR test, Bayesian analyses, detecting diversifying selection.
• Thanksgiving Break
• Class 23: Selection, selective sweeps, review
• Class 24: PSI Blast
• Comp. Lab 13: PSI blast (and dN/dS in MrBayes)
• Class 25: Detecting HGT, using PSI Blast or hmmer to delineate gene families
• Class 26: Detecting HGT in complex genomes, genome based phylogenies, supertree versus supermatrix approaches
• Comp. Lab 14: Emboss, taxplot

Collection of goals after midterm

• Final: Dec. 14, 6pm in GENT 140
  

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