MCB 3421 - Fall 2023

Introduction to Molecular Evolution and Bioinformatics

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

   Teaching Assistant: Daniel Phillips (daniel.s.phillips@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 TLS 301. Lectures will be life streamed, and lecture recordings will become available on huskyCT under Course content.
        Friday's classes will meet in the computer lab located in the TLS 411 .

(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:

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

    Check the Take-Home Exams on HuskyCT
    Link to training questions will be posted here.

IMPORTANT DATES:
      10/02     Share you electronic noteboot with the instructors
        10/11   Midterm, TLS301 at 11.15AM -- tentative date
        11/18-11/26 Thanksgiving break 
        12/08   Last Day of Classes
        12/11   Final at 8am in TLS301

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

Worksheets for Computerlabs
  • Computer-lab assignment 01: Intro to Chimera - Binding Pocket Substrate Interactions
  •    Team based learning 01
  • Computer-lab assignment 02: Aligning divergent sequences and structures in Chimera
  •    Team based learning 02
  • Computer-lab assignment 03: Intein domains and interactions with DNA in Chimera
  •    Team based learning 03
  • Computer-lab assignment 04: Literature databanks and blast searches via web interfaces
  • Computer-lab assignment 05  pdf-version: Intro to Xanadu, PRSS and the transitive property of homology, intro to seaview
  • Computer-lab assignment 06  pdf-version: Dissecting proteins into domains using SeaView, structure prediction using alphafold
  • Computer-lab assignment 07  pdf-version: Cumulative strand bias and mummer plots
  •    Team based learning 07
  • Computer-lab assignment 08  pdf-version: Command line blast and dot plots
  • Computer-lab assignment 09  pdf-version: Trees, ml ratio test, LBA, missing data
  • Computer-lab assignment 10  pdf-version: Estimating trees and model parameters in MrBayes
  • Computer-lab assignment 11  pdf-version: Estimating dN/dS in MrBayes
  • Computer-lab assignment 12  pdf-version: PSI-blast
  • Computer-lab assignment 13  pdf-version: Simple scripts for repetitive tasks - IEP as example / beautiful phylogenies in Figtree
  • Computer-lab assignment 14  pdf-version: Comparing phage genomes using phamerator
    •    
    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