MCB 221 - Fall 2006

Introduction to Molecular Evolution and Bioinformatics

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

Teaching Assistant: Greg Fournier gregory.fournier@huskymail.uconn.edu; with back-up by Pascal Lapierre, pascal.lapierre@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 301 in TLS

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

Reading materials are on WebCT -- if you cannot get access, send your netID to Greg Fournier.

There also will be a discussion board on WebCT. 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 is preferred) that might be useful for the final!

Take Home Quiz/Assignment: #1, #2, #3, #4, #5, #6, #7, #8

Optional Essay Assignment

IMPORTANT DATES:
Midterm: 10/11/2006 in TLS 301
Final: W 12/13/2006 03:30pm - 05:30pm in TLS 301

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, 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) 11

Blue: meets in TLS 301

Class 41: Review Sessions in T115
Class 40: Introns, Phylip, Bayes,
Class 39: Discussion, possibly introns late
Class 38: MrBayes and positive selection
Class 37: Bayes and positive selection
Class 36: Continue Probabilityand ml mapping, puzzle and Mr Bayes
Class 35: Deep view continued, takehome assignment 7
Class 34: Posterior Probability, ml mapping, programs (PHYLIP, PHYML, MrBayes)
Class 33: Tree, Bootstrap, ML
Class 32: Bootstrap, Intro to deep view
Class 31: Movie on thhe tree of life, featuring Carl Woese, Karl Stetter, Karen Nelson and Craig Venter (more info here)
Class 30: Tree, confidence values,
Class 29: Trees in clustal and phylip
Class 28: Tree, building molecular phylogenies.
Class 27: Discussion, recombination, trees
Class 26: PSI BLAST and genome blast with PSSM
Class 24: discussion of the RNA world and in vitro selection / PSI Blast
Class 23: Populations, adaptive sweeps.
Class 22: Genome scale analyses
Class 21: Selection vs Neutral Evolution
Class 20: Coalescence, mutations ...
Class 19: Genefinder and WorkBench
Class 18: Trees continued, review, if time, origin of life research
Class 17: Synteny
Class 16: Review Session
Class 15: Trees, progressive alignemts, types of error
Class 14: UNIX on Macs, multiple alignments with clustalx
Class 13: ATPases and the root. Overview sequence alignment
Class 12: Questions / if time "The tree of life"
Class 11: Dotlet Exercises
Class 10: Inteins, ATPases, // the earliest evidence for life
Class 9: Discussion of Quiz 1, Timeline of the Universe
Class 8: simple Blast searches
Class 7: pan-genomes , life and evolution
Class 6: Friday's results and questions
Class 5: E-values, PRSS, BLAST
Class 4: Similarity/Homology - PRSS - E and P-values
Class 3: Simple exercises with ENTREZ and Web of Science.
Class 2: databank searches, definitions of Life, if time reductionisms.
Class 1: Overview; topics; textbook; reading materials; How will grades be calculated?

Flyer, 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."

Last year's course web page , Cool Links

Send an Email to Peter Gogarten

Go the Gogarten-Lab homepage

MCB 221 - Fall 2006

Introduction to Molecular Evolution and Bioinformatics

Possibility to boost your participation grade: Email questions (multiple choice is preferred) that might be useful for the final!

Take Home Quiz/Assignment: #1, #2, #3, #4, #5, #6, #7, #8

Possibility to boost your participation grade:
Email questions (multiple choice is preferred) that might be useful for the final!