Bioinformatics
- Summer 2007
An
Introduction to Databank Searches, Homology Assessment,
Molecular Phylogenies, Comparative Genome Analyses, 3-D Structure Manipulation
and Comparison
Instructor: J.Peter Gogarten, Dept. Molecular and Cell Biology, University of Connecticut,
Storrs, CT 06269-3125
gogarten@uconn.edu
Where: FH-Mannheim, Building 10, Room No. 406A
When: Thursday,
May 11, 9.30am - Wednesday, May 17, 5pm
Approximate
Timetable
The
Topics listed below will NOT be covered in order.
Topics
and links to more detailed descriptions:
Topic
#1:
Introduction,
Entrez and other databanks
Assignment
at bottom of page
Topic
#2a: Overview on Phylogenetic Reconstruction:
From Databank Searches to Tree Building; Types of Homology
Topic
#2b: How to detect Open Reading Frames
(ORFs), Introns and Exons?
Assignment at bottom
of page
Topic
#3: Homology assessment: When are two sequences homologous?
z-values,
PRSS, BLAST and Psi-BlAST. Searches with Position Specific Scoring Matrices
Among
others we will use PRSS a program from Bill Pearson. This and many other of Bill
Pearson's programs are available from his web page at ftp://ftp.virginia.edu/pub/fasta/.
Assignment at bottom of page
Topic
#4: Multiple Sequence Alignments (clustalw
& co) and
Introduction
to Unix: telnet and FTP
Assignment at bottom of page
Topic
#5: Building distance trees with clustalw,
using treeview
Neighbor
Joining, Bootstrapping
Assignment at bottom of page
Topic
#6: Genome Comparisons
Genomes at NCBI, clusters
of orthologous genes, TAXtable,
Biogagdets, Dotplots,
gene clusters
Assignment
in middle and at bottom of page
Topic
#7: Long branch attraction,
Maximum Likelihood Approaches using TREE-PUZZLE
Testing
trees and models using the maximum likelihood ratio test, Maximum
likelihood mapping
Assignment
in middle and at bottom of page
Topic
#8: Comparison and manipulation of 3D structures:
A) Introduction
to SPdbV, manipulation and display of a single subunit proteins with bound substrate
B) Different approaches
to align similar protein structures using the F-ATPases as an example
C) Comparing divergent proteins with similar structures
D) Inteins - the ultimate selfish gene?
Assignments and exercises are included with each of the sections.
Topic
#9: Predicting positively selected sites using MrBayes.
EXAM
Other class related stuff: Intro
to X-windows, Some Unix commands
Send an Email to Peter Gogarten
Go the Gogarten-Lab homepage