Course Materials for Bioinformatics I
Fall 2003
Study guide for exam:
part 1
General:
What is Bioinformatics I?
Basic Definitions
Useful Websites
2003 NAR Database Issue
2003 NAR Website Issue
Nature Genome Gateway
Class Notes:
local copy of public human genome paper (PDF)
local copy of mouse genome paper (PDF)
Genome Headlines
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.
Recent short
paper about Clustal.
amino acid substitution scores
probabilistic sequence models
Hidden Markov Models
Assignments:
assignment #1