Exercise 1 - Gene Prediction Through Database Searches Go!
- If parts or all of an un-annotated sequence are already stored in some database, searches for
similar sequences can significantly minimize the effort to identify genes in un-annotated sequences.
Find a gene by searching databases for sequences of an un-annotated clone.
Exercise 2 - "Seeing" a Gene In The Human Genome Go!
- Finding genes in databases is one thing. But using databases and the graphical tools they employ
to locate and visualize genes within the human genome is a totally different one!
Exercise 3 - Electronic PCR Go!
- As primer sequences are used to identify target sequences in PCR reactions in vitro, the very same
sequences can be used to identify target sequences in databases. Perform a Blast search and detect the human PV92
locus through electronic PCR in silico. If you thought that you are familiar with the PV92 Alu
polymorphism - be prepared for a big surprise!
Exercise 4 - Search For Information About Genes and Proteins Using Sequence Information Go!
- Databases are rich sources to find all types of gene-related information: protein
sequences, gene regulation data, disease data, genetic variation, gene homology and similarity, etc..
Choose among a variety of sequences to "mine databases".
Exercise 5 - Search For Information About Genes, Proteins and Diseases using Keywords Go!
- Search databases for in-depth information about genes for prions (Mad Cow Disease), the Huntingtin gene, Neurofibromatosis.
Exercise 6 - Genes in Yeast Go!
- The scent of yeast ... (?!?)
Exercise 7 - Genes involved in Cell Communication and Cancer Go!
- Cell-to-cell communication is an integral part of the network of pathways and physiological reactions
that warrant the balanced functioning of all parts within higher organisms. Cell-surface receptors are often involved
in events that lead to the un-checked and, ultimately, malignant growth of cells. Use databases to find and
identify genes involved in this process and determine what exactly causes, on a molecular level, cells
to grow "recklessly". Choose "v-erbb alignment protocol.doc" on the web page you get to for further instructions.
Exercise 8 - Genes involved in Disease
- Mutations can lead to lethal reactions to otherwise benign environmental triggers, incl. drugs and other chemicals.
During the 1950's - 1970's succinylcholine, a muscle relaxant, was used as a popular anaestheticum in surgery
rooms across the US. Succinylcholine was an excellent molecule for this purpose because it did not show any side effects
- except that some people died from it. Using modern genetical methods find out what gene defect is responsible for the
deadly reaction to succinlycholate, which ultimately had to be taken off the market. Design a screening method for the
detection in patients of this defect that would allow to reintroduc this otherwise great anaestheticum that works
fine for more than 98% of patients. (This exercise is not quite ready, yet. However, if you would like to
try it out during the course your instructors would be happy to assist you.)
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