MCB 3421 - Fall 2020
Introduction to Molecular Evolution and Bioinformatics
Instructor: J. Peter Gogarten
(OFFICE: BP room 404, personal room at Webex,
gogarten@uconn.edu)
Teaching Assistant: Sean Gosselin (sean.gosselin@uconn.edu)
The class meets for
Lectures:
Mondays & Wednesdays
11.15 AM-12.05 PM (asynchronous) online at huskyCT,
lectures will be pre-recorded
or recorded. You can go through the lectures
at your own time.
Computer labs and discussion:
Fridays 10:10AM - 11:40AM
or 1:25PM - 2:55PM (synchronous)
online using Webex at https://uconn-cmr.webex.com/meet/jpg02006.
Links to worksheets will be posted below.
Office
hours, question-and-answer sessions:
J Peter Gogarten
Mondays &
Wednesdays 12.05 PM – 12.45 PM or arranged via email.
We have a discussion board on huskyCT.
Contributions on the discussion board will count towards your
participation grade.
Please check the 2020 Syllabus (here)
for information on grading.
The Class Notebook
In addition to huskyCT
and Webex,
we will use a Microsoft
Class Notebook.
- I will use the class notebook to provide access to power point slides,
post summaries and assignments, and provide study materials.
- You will use the class notebook to take notes on the lectures and
computer labs (you can easily post screenshots into the notebook)
AND you will write a short 2-4
sentence reflection on each class: "What was the most interesting thing
I learned today".
- To have access to the notebook as a student, you need to log into log
into MS
Office 365
with your UConn email address as username and your NetID as
password. -- If you cannot get access, send your uconn email
address to gogarten@uconn.edu -
we will try to help you
Possibilities to boost your grade:
- Email
questions (multiple choice preferred) that could be used for
the exams! (this will counts towards participation).
- Optional Essay
Assignment (can take
the place of one take-home exam).
In case you do not see today's assignment, REFRESH
THIS PAGE if this does not help, send an email
- Computer-lab assignment 01:
Intro to chimera - binding pocket substrate interactions
- Computer-lab assignment 02:
Chimera exercise II: Aligning divergent subunits; following a
subunit through the catalytic cycle using the F1-ATPase beta subunit as
example.
- Computer-lab assignment 03:
Chimera exercise III: Aligning divergent proteins (intein with and
without honing endonuclease); protein domains; interactions of the
homing endonuclease with DNA.
- Computer-lab assignment 04:
Databank searches I: pubmed, entrez, google scholar, scopus, blast
- Computer-lab assignment 05:
Terminal, Xanadu, Filezilla, Statistics of sequence comparison, fasta
search
- Computer-lab assignment 06:
Microbial genomes at NCBI, blast from the command line, e-values and %
identity, strand bias
- Computer-lab assignment 07:
Gene plots, strand bias and the origin of replication
- Computer-lab assignment
08: Getting to know Seaview
- Computer-lab assignment
09: Maximum Likelihood, model-test, and MrBayes
- Computer-lab assignment
10: Purifying and diversifying selection
- Computer-lab assignment
11: PSI-blast searches (web and command line)
- Computer-lab assignment
12: Simple scripts to process genome scales of data / Intro to
Figtree
- Computer-lab assignment
13: Dotlet, dot matrix, and mummer plots
Last year's course web page
Send
an Email to J Peter Gogarten
Go the Gogarten-Lab homepage