10. Introduction What is Bioinformatics? Bioinformatics is the field of science in which biology, computer science, and information technology merge into a single discipline Bioinformatics is the electronic infrastructure of Biology Science that encompasses the methods that are used to collect, store, retrieve, analyze, and correlate the mountain of complex biological information. Source: http://ccb.wustl.edu/
12. Introduction The problem: basic understanding of how gene sequences code specific proteins l Lack of the information necessary to completely understand role of DNA in specific diseases or the functions of the thousands of proteins that are produced. The goals: provide scientists with a means to explain: Biological processes. Malfunctions in these processes which lead to diseases. Drug discovery and their mode of action.
17. Deoxyribonucleic Acid (DNA) DNA is found inside a special area of the cell called the nucleus. Because the cell is very small, and because organisms have many DNA molecules per cell, each DNA molecule must be tightly packaged. This packaged form of the DNA is called a chromosome.
18. Deoxyribonucleic Acid (DNA)Composition DNA is made of chemical building blocks called nucleotides. What is DNA made of? The four types of nitrogen bases found in nucleotides are: adenine (A), , thymine (T), guanine (G) and cytosine (C). The order, or sequence, of these bases determines what biological instructions are contained in a strand of DNA. For example, the sequence ATCGTT might instruct for blue eyes, while ATCGCT might instruct for brown.
19. Deoxyribonucleic Acid (DNA)Genes Genes These unique coding sections of DNA that ultimately are transcribed into unique mRNA which are translated into unique proteins are called genes.
20. Deoxyribonucleic Acid (DNA)Function What does DNA do? DNA contains the instructions needed for an organism to develop, survive and reproduce. To carry out these functions, DNA sequences must be converted into messages that can be used to produce proteins, which are the complex molecules that do most of the work in our bodies. To form a strand of DNA, nucleotides are linked into chains, with the phosphate and sugar groups alternating.
21. Deoxyribonucleic Acid (DNA)Replication Replication Chromosomes are located in the nucleus of a cell. DNA must be duplicated in a process called replication before a cell divides. The replication of DNA allows each daughter cell to contain a full complement of chromosomes.
22. Deoxyribonucleic Acid (DNA)Transcription Transcription: The actual information in the DNA of chromosomes is decoded in a process called transcription through the formation of another nucleic acid, ribonucleic acid or RNA.
23. Deoxyribonucleic Acid (DNA)Translation Translation: The information from the DNA, now in the form of a linear RNA sequence, is decoded in a process called translation, to form a protein, another biological polymer.
31. How can computers be useful to biology? First, Computing technology for storing DNA sequences and constructing these latter from fragments. Data storage and access requirements – Study of the organization and evolution of genomes through comparative genome analysis. Visualisation tools and techniques requirements, sequence analysis requirements .
32. How can computers be useful to biology? Structuring and organizing large databases using a common ontology . Access data from different databases using the same query language. (Gene Ontology Consortium ) Many areas of biology use images to communicate their results. Tools and techniques for searching, describing, manipulating and analyzing features within these images.
33. How can computers be useful to biology? Databases maintenance: Need to check consistency of databases for a valid and error free content. Storing protein sequences, their structure as well as their function. Tools and techniques for manipulating protein sequences, protein secondary and tertiary structure prediction…
34. How can computers be useful for biology? Several databases: genome databases, protein sequence databases, metabolic databases, Microarray databases EMBL-EBI (Europe), GenBank-NCBI (USA), DDBJ (Japan) Basic Local Alignment Search Tool (BLAST) program for quick DB searches.
35. How can computers be useful for biology? Several algorithms: Sequence Comparison Algorithms: Needleman-Wunch (global alignment 1970),Smith-Waterman algorithm: Local sequence alignment (1981). BLAST, FASTA, CLUSTALW, MEME...etc http://en.wikipedia.org/wiki/Category:Bioinformatics_algorithms
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37. Data interpretation and generation of hypotheses requires intelligence.
38. AI offers established methods for knowledge representation and “intelligent” data interpretation.
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40. Intelligent Bioinformatics AI and computational intelligence techniques and models: Basic search techniques A*, Branch and Bound, Genetic Algorithms Simulated Annealing Particle Swarm Optimization Neural networks, Support Vector Machines, K nearest neighbors, Hidden Markov Models,….
48. Utilizes a Prolog database to store background biological information.
49. Prolog can inspect biological information, infer knowledge, and make predictions
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51. Intelligent BioinformaticsAn other example: the robot scientist Performance similar to humans Performance significantly better than “naïve” or “random” selection of experiments Ross D. King, et al., Nature, January 2004
52. Challenges Data Fusion or integration: Integration of a wide variety of data sources such as clinical and genomic data will allow us to use disease symptoms to predict genetic mutations and vice versa. The integration of GIS data, such as maps, weather systems, with crop health and genotype data, will allow us to predict successful outcomes of agriculture experiments.
53. Challenges Large-scale comparative genomics. development of tools that can do comparisons of genomes will push forward the discovery rate in this field of bioinformatics. Modeling and visualization of full networks of complex systems predict how the system (or cell) reacts to a drug for example.
54. Challenges Compare complex biological observations, such as gene expression patterns and protein networks. Converting biological observations to a model that a computer will understand. More than that we are more than the sum of the parts….COMPLEXITY
59. Saves time and moneyhttp://smartmoney.com/consumer/index.cfm?story=working-june02
60. OUR CHALLENGE: START WORKING ON BIOINFORMATICS J. Cohen “Computer scientists should be encouraged to learn biology as biologists computer science to prepare themselves for an intellectually stimulating and financially rewarding future.” D. Knuth “…the number of radically new results in pure computer science is likely to decrease, while scientists continue working on biological challenges for the next 500 years….” L. Adleman “..biological life can be equated with computation…”
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