Course Materials for Bioinformatics I
Fall 2004
Study guide for part of the final exam.
Study guide for remainder of the final exam.
General:
What is Bioinformatics I?
Basic Definitions
Introduction to elements of biology -- cells, molecules, genes, functional genomics, microarrays
2003 NAR Database Issue
2003 NAR Web Server Issue
2004 NAR Database Issue
2004 NAR Web Server Issue
Introduction to sequence databasees
Class notes and readings:
Paper on UCSC Genome Browser.
Two images
showing inter-species sequence conservation.
The Browser itself.
Papers on
GenBank and
NCBI.
Notes about PipMaker; more
notes
about PipMaker;
PipMaker publication;
MultiPipMaker
publication.
Notes about alignments scores and Psi Blast.
Notes the dynamic-programming algorithm
for aligning two sequences.
Blast outline and
paper
on Gapped Blast and PSI Blast.
amino acid substitution scores
Methods to determine the number of clusters in a data set
Recent short
paper about Clustal.
probabilistic sequence models
Hidden Markov Models
Genscan paper
Assignments:
assignment #1
assignment #2
phylogeny homework
HemoglobinMAC.nex
HemoglobinMAC.phy
HemoglobinPC.nex
HemoglobinPC.phy
hemoglobin_noalign_2004.txt
hemoglobin_noalign_2004.rtf
Examples of class projects from 2004:
Protein modularity and evolution
Analysis of large deletions in human-chimp genomic alignments
Profile hidden Markov models
Comparison of drosophila genomes
Some addional readings.