MCB 3421 - Fall 2011

Introduction to Molecular Evolution and Bioinformatics

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

   Teaching Assistant: Amanda Dick

   The class meets
        MW 11AM - 11:50AM    AND     Fridays 10AM-11.40AM or 1PM-2.40PM
        NEW !!! Monday's and Wednesday's classes meet in new Classroom Building CB 206 !
        Friday's classes will meet in the computer lab located on the groundfloor of the Chemistry building (T115).

(for directions see here, search for chm or CB, FLYER is here)    

   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 quizes or exams!

Take Home Quiz/Assignments:

Takehome Exam: #1 (pdf/doc/with answers), #2 (pdf/doc/with answers), #3 (pdf/doc/with answers), #4 (pdf/doc/with answers), #5 (pdf/doc/with answers), #6 (pdf/doc/with answers) #7 (pdf/doc/with answers), #8 (pdf/doc/with answers), #9 (pdf/doc/with answers)

Optional Essay Assignment

IMPORTANT DATES:
      Midterm: Monday, Oct. 17, 11am
        Final: (Preliminary Scheduling: Wednesday, December 14th, 10:30 AM - 12:30 pm)
       (Please let me know ahead of time, if you have a conflict for this time. See below for Exam policy.)

Overview on pages accessible from this page

class 1, A1, 2, A2, 3, 4, A3, 5, 6, A4, 7, 8, A5, 9 , 10 , A6, 11, 12, A7, 13, A8, 14, 15, A9, 16, 17, A10, 18, 19, A11, 20, 21, A12, 22, 23, A13, 24, 25, A14

   Red: meets in the Computer Lab in the Chemistry Building (ground floor, T115)
   Blue: meets in Room CB206

• Computerlab 14: Mr Bayes and diversifying selection / review session
• Class 25: Small World Netweorks; the selfish operon theory
• Class 24: MrBayes example, hypothesis testing
• Computerlab 13: Taxplot, geneplot and mummer
• Class 23: MrBayes, ml mapping, selection
• Class 22: Discussion PSI blast, posterior probability
• Computerlab 12: Web and commandline PSI Blast searches.
• Class 21: PSI Blast
• Class 20: Selection and Genetic Drift
• Computerlab 11: Gene Identification Exercises
• Class 19: Population Genetics, Likelihood Ratio Test, Among Site Rate Variation
• Class 18: Phylogenetic reconstruction, LBA
• Computerlab 10: Bootstrap support values and Long Branch Attraction
• Class 17: Trees and support values
• Class 16: Types of homology
• Computerlab 9: Trees - Neighbor joining and parsimony
• Class 15: Intro to trees
• Class 14: Overview on Cladistics, Introns late vs early
• Computerlab 8: Multipel sequence alignment.
• Class 13: Sequence alignements (pairwise, local, global, progressive). Sequence Space.
• Midterm
• Computerlab 7: Sequence alignment using dotlet
• Class 12: Finish genome plots + review session
• Class 11: Gene plot via commandline blast, repetitive sequences,
• Computerlab 6: Blast and commandline blast
• Class 10: Demo of commanline blast
• Class 9: Substitution matrices, the commanline, blast continued
• Computerlab 5: Intro to sequence comparison
• Class 8: Blast searches
• Class 7: Substitutions vs Genetic Distance / Errors in Databanks
• Computerlab 4: Intro to Entrez
• Class 6: Databanks continued
• Class 5: Inteins as an example for molecular parasites, Databanks
• Computerlab 3: Inteins, splicing and homing endonuclease domain in SPDBV
• Class 4: Natural selection, genetic drift, selfish genes. The Tree-of-Life.
• Class 3: Natural selection, genetic algorithms and sequence space
• Computerlab 2: Aligning protein structure in SPDBV
• Class 2: Bioinformatics, Molecular Evolution, Homology
• Computer lab 1: Intro to SPDBV
• Class 1: Overview; topics; textbook; reading materials; How will grades be calculated?

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

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"

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.

Exam policy When students are forced to miss a final examination due to illness, accident, death in the family or other unavoidable reasons they can come to the Office of Student Services & Advocacy to receive approval to arrange another exam time with their instructor. Students should present appropriate documentation to support their request. With other exams and assignments which are required during the semester students bring their documentation of extenuating circumstances directly to their instructors. There are no make-up exams for the take-home exam. If you need to reschedule your final, please let your instructor know in a timely manner.

Send an Email to Peter Gogarten

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