MCB 3421 - Fall 2008

Introduction to Molecular Evolution and Bioinformatics

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

Teaching Assistant: Tim Harlow t.harlow@uconn.edu;

   The class meets
        MW 11AM - 11:50AM    AND     Fridays 10AM-11.40AM or 1PM-2.40PM
        Monday's and Wednesday's classes meet in Room 323 of the Engineering II building
        Friday's classes will usually meet in the computer lab located on the groundfloor of the Chemistry building (T115).

(for directions see here, search for chm or E2)

Reading materials will be posted on huskyCT -- if you cannot get access by Wednesday, send your netID to Tim Harlow.

There also will be a discussion board on huskyCT. Contributions you make there 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 quizes or exams!

Take Home Quiz/Assignments:

Quiz #1; Quiz #2; Quiz #3 (answers); Quiz #4 (answers), Quiz #5 (ans), Quiz #6(ans), Quiz #7(Ans), Quiz #8 (Ans), Quiz #9 Ans

Optional Essay Assignment

IMPORTANT DATES:
      Midterm: October 20th in Room 323 EngII
        Final: (Preliminary Scheduling) Wednesday December 10th, 3.30 - 5.30 (info on emergency closings)
       (Please let me know ahead of time, if you have a conflict for this time)

Overview on pages accessible from this page

class 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40

Red: meets in the Computer Lab in the Chemistry Building (ground floor, T115)
Blue: meets in Room 323 Engineering II

Class 40: MrBayes - Introductory Exercises
Class 39: detecting positive and purifying selection, discussion of take home exams.
Class 38: Probability mapping and detecting positive slection
Class 37: Distance matrix, bootstrap and parsimony analyses - long branch attraction.
Class 36: Bayes aand ASRV
Class 35: Building trees. support values
Class 34: PSI blast exercises
Class 33: PSI blast
Class 32: Neutral Evolution
Class 31: Trees with clustal and phylip
Class 30: In vitro selection, recombination and linkage between protein evolution and the encoding genes
Class 29: genes, populations and selection
Class 28: TaxPlot, TaxTable and Mummer
Class 27: Gene duplications continued
Class 26: gene duplications, types of homology
Class 25: Intron/Exon detection, prediction of membrane spanning helices, molecular workbench
Class 24: Tree terminology, part 2
midterm
Class 23: Finging ORFs, Gene Plots, and Synteny
Class 22: Tree terminology, part 1
Class 21: Trees, terminology and coalescence
Class 20: clustal and jalview
Class 19: clustal (and trees if time)
Class 18: return quiz, discuss dotlet, and exon shuffling (broken projection equipment)
Class 17: dotlet, inspecting protein protein and protein DNA alignments
Class 16: dotlet, optimal alignmetns, intro to trees part 1
Class 15: blastall discussion, optimal pairwise alignment
Class 14: simple blast and blastall searches
Class 13: blast and the command line
Class 12: multiple substitutions, dot matrix representation
Class 11: simple homology searches
Class 10: Z scores, expectations and probabilities
Class 9: Discussion and review
Class 8: Simple Databank searches using Entrez and Web of Science
Class 7: Databanks, Entrez
Class 6: Aligning pdb file in Deep view, review of the homology concept
Class 5: Aligning protein pdb files in deep view
Class 4: Why is an evolutionary perspective important?
Class 3: Using Deep View
Class 2: protein structure, protein evolution, spdbv
Class 1: Overview; topics; textbook; reading materials; How will grades be calculated?

Topics

Plagiarism for writing assignments, and "collaborations" on take-home exams and writing assignments will not be tolerated!
In case of misconduct you will receive an F for the assignment, AND the F will counted towards the final grade. See class 1 for info on how the grade will be calculated.

From the UConn student conduct code:

"Academic misconduct includes, but is not limited to, providing or receiving assistance in a manner not authorized by the instructor in the creation of work to be submitted for academic evaluation (e.g., papers, projects, and examinations); any attempt to influence improperly (e.g., bribery, threats) any member of the faculty, staff, or administration of the University in any matter pertaining to academics or research; presenting, as one’s own, the ideas or words of another for academic evaluation; doing unauthorized academic work for which another person will receive credit or be evaluated; and presenting the same or substantially the same papers or projects in two or more courses without the explicit permission of the instructors involved.
A student who knowingly assists another student in committing an act of academic misconduct shall be equally accountable for the violation, and shall be subject to the sanctions and other remedies described in The Student Code."

Exam policy from the dean of students:

“Attention Students. Final exam week for Fall 2008 takes place from Monday, December 8, through Saturday, December 13. Students are required to be available for their exam during that time. Students must visit the Dean of Students Office if they cannot make their exam. The DOS will give the student his or her instructions thereafter. Please note: vacations, previously purchased tickets or reservations, weddings (unless part of the wedding party), and other large or small scale social events, are not viable excuses for missing a final exam. Please contact the Dean of Students office with any questions. Thank you in advance for your cooperation.”

Last year's course web page, Cool Links

Send an Email to Peter Gogarten

Go the Gogarten-Lab homepage