What is bioinformatics?

1. What is bioinformatics? Daniel Svozil

2. Definition • NCBI • Bioinformatics is the field of science in which biology, computer science, and information technology merge into a single discipline. The ultimate goal of the field is to enable the discovery of new biological insights and to create a global perspective from which unifying principles in biology can be discerned. • Wikipedia.org • The application of information technology and statistics to the field of molecular biology. • The creation and advancement of databases, algorithms, computational and statistical techniques, and theory to solve formal and practical problems arising from the management, analysis and interpretation of biological data. http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html

3. Extraction of biological knowledge from data convert data to knowledge generate new hypotheses Experimental Data Knowledge From public databases design new experiments

4. Omes genome – DNA sequence in an organism transcriptome – mRNA of an entire organism proteome – all proteins in an organism metabolome – all metabolites in an organism interactome – all molecular interactions in an organism Organism Cell Tissue architectures Cell interactions Sigaling …… Genome Transcriptome Reactome Proteome Metabolome

5. Omes and Omics • Genomics • Primarily sequences (DNA and RNA) • Databanks and search algorithms • Supports studies of molecular evolution • Proteomics • Sequences (Protein) and structures • Mass spectrometry, X-ray crystallography • Databanks, knowledge bases, visualization • Functional Genomics (transcriptomics) • Microarray data • Databanks, analysis tools, controlled terminologies • Systems Biology (metabolomics) • Metabolites and interacting systems (interactomics) • Graphs, visualization, modeling, networks of entities

6. Genomics Transcriptomics Proteomics Metabolomics Interactomics …… Sequencing Microarrays LC/MS NMR Two hybrid …… includes measured by “Omics” High-throughput High-noise their data are Advanced pre-processing techniques To reduce noise Biological knowledge Medical knowledge Improved health Techniques to analyze high-dimensional data and knowledgebases Reliable high-throughput information source: Bios 560R Introduction to Bioinformatics, userwww.service.emory.edu/~tyu8/560R/560R_1.pptx

7. Key reasearch in bioinformatics • sequence bioinformatics • structural bioinformatics • systems biology • analysis of biological pathways to gain e.g. the understanding of disease processes

8. 21st century – complex systems • Designing (forward-engineering) • Understanding (reverse-engineering) • Fixing • Why is it so complex? • Can we make a sense of this complexity? • How is it robust? http://yilab.bio.uci.edu/ICSB2007_Tutorial_AM1.htm

9. studying genomes

10. Studying DNA

11. Enzymes for DNA manipulation • Before 1970s, the only way in which individual genes could be studied was by classical genetics. • Biochemical research provided (in the early 70s) molecular biologists with enzymes that could be used to manipulate DNA molecules in the test tube. • Molecular biologists adopted these enzymes as tools for manipulating DNA molecules in pre-determined ways, using them to make copies of DNA molecules, to cut DNA molecules into shorter fragments, and to join them together again in combinations that do not exist in nature. • These manipulations form the basis of recombinant DNA technology.

12. Recombinant DNA technology • The enzymes available to the molecular biologist fall into four broad categories: • DNA polymerase – synthesis of new polynucleotides complementary to an existing DNA or RNA template • Nucleases – degrade DNA molecules by breaking the phosphodiester bonds • restriction endonucleases (restriction enzyme) – cleave DNA molecules only when specific DNA sequences is encountered • Ligases – join DNA molecules together • End modification enzymes – make changes to the ends of DNA molecules

13. source: Brown T. A. , Genomes. 2nd ed. http://www.ncbi.nlm.nih.gov/books/NBK21129/

14. DNA cloning • DNA cloning (i.e. copying) – logical extension of the ability to manipulate DNA molecules with restriction endonucleases and ligases • vector • DNA sequence that naturally replicates inside bacteria. • It consists of an insert (transgene) and larger sequence serving as the backbone of the vector. • Used to introduce a specific gene into a target cell. Once the expression vector is inside the cell, the protein that is encoded by the gene is produced by the cellular-transcription and translation machinery ribosomal complexes. • plasmid (length of insert: 1-10 kbp), cosmid (40-45 kbp), BAC (100-350 kbp), YAC (1.5-3.0 Mbp)

15. Vectors • plasmid • DNA molecule that is separated from, and can replicate independently of, the chromosomal DNA. • Double stranded, usually circular, occurs naturally in bacteria. • Serves as an important tool in genetics and biotechnology labs, where it is commonly used to multiply (clone) or express particular genes. • BAC (bacterial artificial chromosome) • It is a particular plasmid found in E. coli. A typical BAC can carry about 250 kbp. source: wikipedia

16. restriction endonuclease ligase DNA cloning source: Brown T. A. , Genomes. 2nd ed. http://www.ncbi.nlm.nih.gov/books/NBK21129/

17. PCR – Polymerase chain reaction • DNA cloning results in the purification of a single fragment of DNA from a complex mixture of DNA molecules. • Major disadvantage: it is time-consuming (several days to produce recombinants) and, in parts, difficult procedure. • The next major technical breakthrough (1983) after gene cloning was PCR. • It achieves the amplifying of a short fragment of a DNA molecule in a much shorter time, just a few hours. • PCR is complementary to, not a replacement for, cloning because it has its own limitations: the need to know the sequence of at least part of the fragment.

18. Mapping genomes

19. What is it about? • Assigning/locating of a specific gene to particular region of a chromosome and determining the location of and relative distances between genes on the chromosome. • There are two types of maps: • genetic linkage map – shows the arrangement of genes (or other markers) along the chromosomes as calculated by the frequency with which they are inherited together • physical map – representation of the chromosomes, providing the physical distance between landmarks on the chromosome, ideally measured in nucleotide bases • The ultimate physical map is the complete sequence itself.

20. Genetic linkage map • Constructed by observing how frequently two markers (e.g. genes, but wait till next slides) are inherited together. • Two markers located on the same chromosome can be separated only through the process of recombination. • If they are separated, childs will have just one marker from the pair. • However, the closer the markers are each to other, the more tightly linked they are, and the less likely recombination will separate them. They will tend to be passed together from parent to child. • Recombination frequency provides an estimate of the distance between two markers.

21. Genetic linkage map • On the genetic maps distances between markers are measured in terms of centimorgans (cM). • 1cM apart – they are separated by recombination 1% of the time • 1 cM is ROUGHLY equal to physical distance of 1 Mbp in human Value of genetic map – marker analysis • Inherited disease can be located on the map by following the inheritance of a DNA marker present in affected individuals (but absent in unaffected individuals), even though the molecular basis of the disease may not yet be understood nor the responsible gene identified. • This represent a cornerstone of testing for genetic diseases.

22. Genetic markers • A genetic map must show the positions of distinctive features – markers. • Any inherited physical or molecular characteristic that differs among individuals and is easily detectable in the laboratory is a potential genetic marker. • Markers can be • expressed DNA regions (genes) or • DNA segments that have no known coding function but whose inheritance pattern can be followed. • genes – not ideal, larger genomes (e.g. vertebrates) → gene maps are not very detailed (low gene density)

23. Genetic markers • Must be polymorphic, i.e. alternative forms (alleles) must exist among individuals so that they are detectable among different members in family studies. • Variations within exons (genes) – lead to observable changes (e.g. eye color) • Most variations occur within introns, have little or no effect on an organism, yet they are detectable at the DNA level and can be used as markers. • restriction fragment length polymorphisms (RFLPs) • simple sequence length polymorphisms (SSLPs) • single nucleotide polymorphisms (SNPs, pronounce “snips”)

24. RFLPs • Recall that restriction enzymes cut DNA molecules at specific recognition sequences. • This sequence specificity means that treatment of a DNA molecule with a restriction enzyme should always produce the same set of fragments. • This is not always the case with genomic DNA molecules because some restriction sites exist as two alleles, one allele displaying the correct sequence for the restriction site and therefore being cut, and the second allele having a sequence alteration so the restriction site is no longer recognized. source: Brown T. A. , Genomes. 2nd ed. http://www.ncbi.nlm.nih.gov/books/NBK21129/

25. SSLPs • Repeat sequences that display length variations, different alleles contain different numbers of repeat units (i.e. SSLPSs are multi-allelic). • variable number of tandem repeat sequences (VNTRs, minisatellites) • repeat unit up to 25 bp in length • simple tandem repeats (STRs, microsatellites) • repeats are shorter, usually di- or tetranucleotide source: Brown T. A. , Genomes. 2nd ed. http://www.ncbi.nlm.nih.gov/books/NBK21129/

26. SNPs • Positions in a genome where some individuals have one nucleotide and others have a different nucleotide. • Vast number of SNPs in every genome. • Each SNP could have potentially four alleles, most exist in just two forms. • The value of two-allelic marker (SNP, RFLP) is limited by the high possibility that the marker shows no variability among the members of an interesting family. • The advantages of SNP over RFLP: • they are abundant (human genome: 1.5 millions of SNPs, 100 000 RFLPs) • easire to type (i.e. easier to detect)

27. more at http://www.informatics.jax.org/silver/chapters/7-1.shtml Genome maps relative locations of genes are established by following inheritance patterns visual appearance of a chromosome when stained and examined under a microscope the order and spacing of the genes, measured in base pairs sequence map source: Talking glossary of genetic terms, http://www.genome.gov/glossary/