MCB 3421 - Fall 2024

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. 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.

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
        10/09   Midterm, TLS301 at 11.15AM
        11/23-12/1 Thanksgiving break 
        12/06   Last Day of Classes
        Final: Monday 12/9 at 8.00AM 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  pdf-version: Intro to Chimera - Binding Pocket Substrate Interactions
  •    Team based learning 01 (comments in the slides at the end)
  • Computer-lab assignment 02  pdf-version: Aligning divergent sequences and structures in ChimeraX, morphing subunits in the catalytic cycle
  • Computer-lab assignment 03  pdf-version: Characterizing intein domains using chimeraX / predict protein structures / protein-dna interactions
  •    Team based learning 02 (comments in the slides at the end)
  • Computer-lab assignment 04  pdf-version: Databanks in Entrez, simple blast searches at the NCBI and at phagesDB
  • Computer-lab assignment 05  pdf-version: Intro to Xanadu, PRSS, the transitive property of homology, seaview
  • Computer-lab assignment 06  pdf-version: Genomes at the NCBI, GC Skew
  • Computer-lab assignment 07  pdf-version: Mummer, within genome recombination and dot plots
  • Computer-lab assignment 08  pdf-version: Comparing divergent genomes using blastp
  • Computer-lab assignment 09  pdf-version: Dissecting alignments in Seaview, Neighbor Joining trees, predicting intein structures in collabfold
  • Computer-lab assignment 10  pdf-version: Likelihood Ratio Test, Long Branch Attraction
  • Computer-lab assignment 11  pdf-version: MrBayes and Tracer
  • Computer-lab assignment 12  pdf-version: Identification of sites under positive selection
  • Computer-lab assignment 13  pdf-version: PSI-blast, PSSMs, hunting selfish genetic elements in eukaryotic genomes
  • Computer-lab assignment 14  pdf-version: Scripts for repetitive tasks, Figtree
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    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