MCB 3421 - Fall 2021

Introduction to Molecular Evolution and Bioinformatics

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

Teaching Assistant: Sophia Gosselin (sophia.gosselin@uconn.edu)

   The class meets
        MW 11.15AM - 12.05PM    AND     Fridays 10.10.AM-11.40AM or 1.25PM-2.55PM
        Monday's and Wednesday's classes meet in UTEB150. Live streamed here.
        Friday's classes will meet in the computer lab located in the Whetton Graduate Center (Room 300A).

(for directions follow the above links to the UConn campus map)

Reading materials will be posted on huskyCT -- if you cannot get access, send your netID to gogarten@uconn.edu

We also will have a discussion board on huskyCT. Contributions on the discussion board will count towards your participation grade.

REFRESH THIS PAGE EVERY TIME YOU VISIT IT

Possibilities to boost your grade:

Email questions (multiple choice preferred) that could be used for the exams! (counts towards participation).
Optional Essay Assignment (can take the place of one take-home exam).
Optional Research Project to Accompany the Course.

Exam Questions for Self Study and Correct Answers from Take-Home Exams:

   Check the Take-Home Exams on HuskyCT
    Additional questions for midterm study

IMPORTANT DATES:
      10/6 Share you electronic noteboot with the instructors
        10/20 Midterm, UTEB 150 at 11.15AM
        11/21-11/28 Thanksgiving break
        12/10 Last Day of Classes
        12/13 Final, UTEB 150 at 8.00AM

(Please let me know ahead of time, if you have a conflict for this time. See syllabus for exam policy.)

Running list of Goals, Links to Slides and Study Materials, Assignments
- discuss if things are not clear.
Note: assignments will NOT be copied to huskyCT

Worksheets for Computerlabs

Computer-lab assignment 11: Measuring positive selection using dN/dS in MrBayes

Computer-lab assignment 10: MrBayes, estimating trees and parameters (inteins versus exteins), High Probability Density Intervals

Computer-lab assignment 09: Phylogenetic reconstruction, Maximum Likelihood Ratio Test, Long Branch Attraction

Computer-lab assignment 08: Dotplots and intro to Seaview

Computer-lab assignment 07: Strand bias and gene plots. Via webex https://uconn-cmr.webex.com/meet/jpg02006

Computer-lab assignment 06: Database searches using BLAST+ executables / possibly GC Skew

Computer-lab assignment 05: Statistics of Sequence Comparison (/ Dotplots)

Computer-lab assignment 04: Databank Search Exercise Part A

Computer-lab assignment 03: Exploring Intein Structures in Chimera

Computer-lab assignment 02: Aligning Divergent Proteins; Following Structural Changes Through a Catalytic Cycle

Computer-lab assignment 01: Intro to Chimera - Binding Pocket Substrate Interactions

REFRESH THIS PAGE EVERY TIME YOU VISIT IT

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

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

Go here for course pages from previous years
Send an Email to Peter Gogarten

Go the Gogarten-Lab homepage