Introduction to Bioinformatics
for Medical Research
This course introduces a wide range of bioinformatics tools and concepts for application in medical research.
The course is data-centric and focuses on practical use but introduces a few basic theoretical issues too.
The course was delivered during April - July 2003 to members of the Technion Faculty of Medicine by Gideon Greenspan, with
Oleg Rokhlenko as teaching assistant. Each week consisted of a 1 hour lecture, followed by a 2 hour hands-on tutorial.
| Week |
Lecture |
Tools |
| 1 |
Introduction to Bioinformatics |
PubMed, OMIM, BioMail |
| 2 |
Introduction to Data Formats |
GenBank, SWISS-PROT, GeneCards |
| 3 |
Genomic Sequence Alignment |
BLASTN, Pairwise BLAST, FASTA |
| 4 |
Protein Sequence Alignment |
SIM-Prot, BLASTP |
| 5 |
Advanced BLAST |
PSI-BLAST |
| 6 |
Motifs and Motif Finding |
MEME/MAST |
| 7 |
Motif Databases and Gene Finding |
TRANSFAC, BLOCKS, ORFFinder, GenScan |
| 8 |
Multiple Alignment and Phylogeny |
ClustalW, Phylip, Phylodendron |
| 9 |
Protein Secondary Structure |
PHDsec, PSIPRED |
| 10 |
Protein Tertiary (3D) Structure |
PDB, TOPITS, GenTHREADER, SCOP |
| 11 |
Microarrays and Expression Data |
EPClust, GEO |
| 12 |
The Human Genome Project |
UCSC Genome |
| 13 |
Probe Design and Gene Networks |
Oligodb, Primer3, KEGG |
| 14 |
Genetic Mapping |
|