1. Information Aspects of Nucleic Acids Measurement Technologies Description of nucleic acid measurement technologies Algorithmic, optimization, data analysis problems introduced by these new technologies

2. General Topics Optimization of the information measured in an assay or a set of assays. (Expression probe design) Optimization of information to resource ratio in molecular level assays. (Multiplexed genotyping assays) Biologically driven data analysis (Analysis of gene expression data) Algorithms for raw data interpretation (SBH, RE mapping)

3. Nucleic Acid Measurement Technologies (examples) Array based hybridization assays (DNA chips) MassSpectrometry based techniques Restriction enzyme fragmentation and length separation Large scale sequencing

4. A Few Basic Concepts of Molecular Biology DNA Proteins The central dogma of cellular biology DNA as a sequence of bases Watson-Crick –ery

5. Central Dogma Transcription mRNA Cells express different subset of the genes In different tissues and under different conditions Gene (DNA) Translation Protein

6. DNA Carries the code for cellular functioning Variation in the code is the source for variation in properties Disease and disease susceptibility can be caused by changes in the DNA. DNA is the same for all cells of an individual.

7. mRNA and Proteins Execute the code Relative levels are different in different cells, depending on function and condition Are indicative of the state of the cell

8. Watson-Crick Complimentarity A binds to T C binds to G AATGCTTAGTC TTACGAATCAG Perfect match AATGCGTAGTC TTACGAATCAG One base mismatch

9. FISH Fluorescence In-Situ Hybridiztion Fluorecsently labeled probes hybridize to specific chromosomal locations. Example application: low resolution localization of an EST.

10. Array Based Hybridization Assays (DNA Chips) Unknown sequence (target) Many copies. Array of probes

11. Target hybs to WC complimentary probes only Therefore – the fluorescence pattern is indicative of the target sequence. Array Based Hyb Assays

12. Thermal Ink Jet Arrays, by Agilent Technologies cDNA array, Inkjet deposition In-Situ synthesized oligonucleotide array. 25-60 mers.

13. Expression Profiling Given a set of genes of interest, measure the quantities of the corresponding mRNA, in cells in various conditions. Assumptions: base sequences are known Fluorescence levels are linear with expression levels Example computational problem: design specific and sensitive probes.

14. Specific Probes … Input: Querry sequence (m:500-2000). Background message (total length of  50Mb). Probe length (20-70). Output: For each probe candidate, its distance to the background message. m

15. In future lectures and mini-projects   we will discuss/study information problems related to designing hybridization based assays and to the interpretation and data analysis of the results.

16. SBH