MCB 372 / EEB 372 Computer Methods in Molecular Evolution
MCB 371 / EEB 371 Current Topics in Molecular Evolution
Organizational Meeting and Class 1
Usually:
Mondays: demonstrations, 20 minute student presentation, discussions and lecture
Wednesdays: exercises and assignments
Requirements and basis for grading:
- 20% participation and assignments
-
email results to instructor/TA or hand in hard copy before next Wednesday - 20% Independent Student Project:
COMPILE, ANALYSE A DATASET OF YOUR CHOICE;
Hand in WRITTEN summary of project, 15 minute oral summary during last week of classes - 20% each: Two written exams (in-class and take-home portion, or take home portion only)
- 20% One 15 Minute presentation
in Monday section.
HOMEWORK, INDEPENDENT STUDENT PROJECT, AND PRESENTATION ARE REQUIRRED OF EVERY PARTICIPANT, REGARDLESS OF STATUS (credit, audit, or "sit in")
Examples for Independent Student Projects:
- Evolution of RubisCO and other enzymes of the Calvin cycle (archaeal genome)
- Evolution of Fructose bis Phosphate synthesizing enzymes (ATP and PP using enzymes)
- Evolution of TUBULINS and TUBULIN related eubacterial and archaeal proteins
- Histones and histone homologues in archaea and eubacteria
- Actin & intermediate filaments
- Aminoacyl tRNA synthases
- H+ATPase subunts (in particular homologues to sub I, Sub A and B and proteolipid)
- P-ATPases: Relation among different ion specificities, homologues, orthologues to archaeal P-types?
- Inteins-vertical versus horizontal transmission
- Origin of the photsynthetic machinery
- Evolution of phycobilisomes
- Evolution of cyanobacteria
Please don't hesitate to discuss your choice of project with the instuctors
or with the TA.
The earlier you decide on a topic the better!
The course will cover the following topics:
- databank searches, BLAST and iterative BLAST searches,
- sequence alignment, sequence alignment using 3-D information,
- statistical analyses of sequence data,
- phylogenetic reconstruction using parsimony -, distance matrix -, maximum likelihood, bayesian inference and other methods
- likelihood ratio tests for model selection
- Assessment of confidence using maximum likelihood mapping, bootstrapping,
Bremer support/decay index, Bayesian posterior probabilities, and split
decomposition
The following programs will be used:
NCBI webpages, ClustalX, Swiss Protein Data Bank Viewer, Phylip, TREE-PUZZLE, PAUP*, MrBayes
GENERAL INFORMATION
After class you should backup your personal files to a ZIP disk or on to a mainframe or UNIX account.
Having an account on a UNIX machine (e.g., SP) might be a good idea, but is not required.
!!!Warning!!!
The course is designed to provide hands on experience in molecular data
analyses with respect to molecular evolution. Past experiences with unprepaired
students compelled us to offer this this course in conjunction with a
lecture/seminar style course that explores the theoretical fondations
of the different applications. Every student is required to show up for
both the lab exercises and the lectures and seminars!
The course does not
provide an overview on computer applications in molecular biology in general
nor does it attempt to provide an overview on Bioinformatics. The focus
is on different aspects of molecular evolution, while discussions among
students are encouraged, this is not a seminar to expound extensively
on the virtues of cladistic analyses.
Students will need to spend time in the computer lab in addition to the scheduled class period, and students that did not have prior exposure to methods used in phylogenetic reconstruction will need to spend some time reading and studying.