MCB 221 - Fall 2007

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 233 in the Young Building

(for directions see here, search for Young)

   Friday's classes will usually meet in the computer lab located on the groundfloor of the Chemistry building (T115).

   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/Assignment:

Take home quiz #1 ,
#2 ,
#3 (#3 with a few selected answers),
#4 (#4 with answers)
Take home quiz #5 ,
#6,
#7 (#7 with selected answers),
#8 (#8 with answers),
#9 (#9 with answers)

Optional Essay Assignment

IMPORTANT DATES:
        Midterm: October 15th in Young Building room 233, 11am
        Final: Friday December 14th, 08:00 AM~10:00 AM; in Young Building room 233
        In case of a late opening due to weather conditions, the exam will take place at 8.30pm, same day. same room. (More here and here)
        (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 Young Building Room 233

• Class 40: Analyses using MrBayes and Deep View
• Class 39: Review session
• Class 38: Positive selection
• Class 37: Microarray Exercises
• Class 36: Microarrays
• Class 35: discussion of quizz6, positive selection, MicroarraysI
• Class 34: Intro to the SPDBV
• Class 33: Quartets, Simplex , ML rariontest
• Class 32: Species versus Gene Trees, LBA, MrBayes
• Class 31: Phylip and Long Branch Attraction
• Class 30: Building trees continued
• Class 29: trees bootstrap Phylip
• Class 28: Trees with clustal and phylip
• Class 27: Neutral evolution
• Class 26: Discussion of PSI blast, commandline populations
• Class 25: PSI-Blast
• Class 24: PSI-Blast, commandline, ...
• Class 23: Questions and Population genetics
• Class 22: Comparative genome analyses
• Class 21: Exam questions / In vitro evolution
• MIDTERM
• Class 20: GeneScan and Molecular Workbench
• Class 19: Review session (possibly continuation class 19)
• Class 18: Cladistic terminology, trees, roots and topology
• Class 17: ORF finding and Synteny
• Class 16: Questions, terminology, if time sequence space.
• Class 15: Tree of Life, Gene transfer
• Class 14: sequence alignment - Clustalx and Jalview
• Class 13: principle of progressive alignment and Tree/Coral of Life
• Class 12: Dotlet and Jalview demos
• Class 11: Dotlet exercises
• Class 10: Needleman Wunsch alignment, ATPases
• Class 9: evolution as algorithm, sequence alignment overview, probability density, discussion.....
• Class 8: BLAST searches
• Class 7: Evolution as algorithm - other processes occurring in natural evolution
• Class 6: Homology, sequence space, Statistics of sequence comparison
• Class 5: Statistics of sequence comparison
• Class 4: data banks with and without gatekeeper, PRSS, FASTA, E-values and significance,
• Class 3: literature and entrez databanks
• Class 2: Questions from class1, overview on databanks,
• Class 1: Overview; topics; textbook; reading materials; How will grades be calculated?

"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."

Send an Email to Peter Gogarten

Go the Gogarten-Lab homepage