MCB 3421 - Fall 2014

Introduction to Molecular Evolution and Bioinformatics

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

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

   The class meets
        MW 11.10AM - 12.05AM    AND     Fridays 10.10.AM-11.40AM or 1.25PM-2.55PM
        Monday's and Wednesday's classes meet in the YOUNG Building 327;
        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 YNG)    

   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

Possibility to boost your participation grade:
  Email questions (multiple choice preferred) that could be used for the quizzes or exams!

Take Home Quiz/Assignments:

Take-home Exams: #1 (doc/pdf/answers), #2(doc/pdf/answers), #3 (doc/pdf/answers), #4 (doc/pdf/answers), #5 (doc/pdf/answers), #6 (doc/pdf/answers), #7 (doc/pdf/answers), #8(doc/pdf/answers), #9(doc/pdf/answers)

Optional Essay Assignment

IMPORTANT DATES:
      Midterm: Wednesday, Oct. 8, 11.10AM- 12.05PM
       Final: (preliminary) Wednesday, Dec. 10, 10.30am - 12.30pm
       (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 YNG 327

• Comp. Lab 14: taxplot, mummer, emboss
• Class 26: Quartet decomposition & review session
• Class 25: Supertree vs supermatrix approaches
• Comp. Lab 13: PSI Blast
• Class 24: Selection in human populations &PSI Blast
• Class 23: Types of selection
• Comp. Lab 12: MrBayes exercises
• Class 22: Role of HGT in evolution, types of selection
• Class 21: LBA discussion, neutral theory
• Comp. Lab. 11: Reconstructing phylogenies - LBA
• Class 20: Reasons for phylogenetic conflict.
• Class 19: Trees and human evolution
• Comp. Lab 10: Intro to building phylogenetic trees
• Class 18: phylogenetic analyses, continued
• Class 17: Intro to phylogenetic reconstruction
• Comp. Lab 9: Multiple Sequence Alignments
• Class 16: Multiple Sequence Alignments
• Class 15: Natural taxonomy - intons early versus late
• Comp. Lab 8: Dotlet and Jalview exercises
• Class 14: Sequence space and terminology used in cladistics
• Class 13: Genome rearrangement and expansion
• Comp. Lab. 7: Unix and Commandline Blast cont. - gene plots
• Midterm
• Class 12; Review and Discussion of Blast and Unix and ..
• Comp. Lab. 6: Unix and Commandline Blast
• Class 11: Command line blast and simple perl scripts continued
• Class 10: Dayhoff, blast, and the command line
• Comp. Lab 5: Satistics of Sequence Comparisons
• Class 9: E and P-values, false positves, false negatives.
• Class 8: Exponential functions, open pan genomes / decay of significance
• Comp. Lab 4: Databank searches, part A: ENTREZ/BLink
• Class 7: Databanks, Entrez / Reticulate Evolution
• Class 6: History of Earth and tree/web of life.
• Comp. Lab 3: Aligning divergent domains in SPDBV
• Class 5: Evolution, natural selection, what else? Number of substitutions versus %sequence divergence. Intro to inteins.
• Class 4: Evolution -> Gaia
• Comp. Lab 2: Aligning multiple layers in SPDBV
• Class 3: Molecular evolution meets bioinformatics
• Comp. Lab 1: Intro to SPDBV
• Class 2: Homology, similarity, function
• Class 1: Overview; topics; textbook; reading materials; How will grades be calculated?

Topics - If you have suggestion for additional topics, please let me know,

Syllabus <- (see for grade calculation, exam policy, and penalties for academic misconduct)

From Community Standards:

"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"

Send an Email to Peter Gogarten

Go the Gogarten-Lab homepage