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Workshop in Bioinformatics 2010 Class # 75321 Class 8 March 2010
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(Molecular) Bioinformatics Development (Computational Biology) New algorithms and statistics to assess biological information Tools for access and management different types of information (DB, Models, Maps..) User view (applied Bioinformatics) Analysis: interpretation of various types of data (nt, aa, domains, RNAs, signatures, 3D-structures) Statistical methods Applying predictions methods (from the shelf) Applying tools (web, programs…)
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What do you mean by “data”… Raw (primary) Processed (analyzed) Integrated (systems)
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What do you mean “raw data”… Raw (primary) Data Sequences RNA (many types) DNA Genome Variations SNP Mutations Copy Number Variations (CNV)
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What do you mean “raw data”… Rate - Raw (primary) Data HM1: Identify 2 areas with a similar (?) trend
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The level of resolution: the ‘basic unit’ example DNA Nucleotide to Genome level NOTE: Not always the technology identify nucleotide in the DNA HW2: provide an example…list the technology
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The level of resolution: the ‘basic unit’ example DNA Nucleotide to Genome level Technology: DNA / RNA SEQUENCING Nucleotide level
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DNA Sequencing “Classical” (Sanger)
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The level of resolution: the ‘basic unit’ example DNA TECNOLOGY definitions: Nucleotide (1) Run (400-800) ABI –Sanger fluorescence capillary Reads (35-400) SOLEXA and 454 (WGS) – BUT millions in parallel
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ABI 3700 96x700 bases Scale: capillary tech RUNs New technology “454” technology (not in this class)
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The level of resolution: the ‘basic unit’ example DNA FUNCTIONAL / Assembly definition (more) SNP (1) Indel (1-1000s) human genome -average 5 bp EST (300-700) Gene (1000 bacteria; 100,000 human; huge range) Contig- 500,000, huge range / BacTig >10 6 Chromosome: Bacteria: 4*10 6, Human: 50- 250*10 6 Genome: HUGE ranges from virus 5*10 3 to frog 5*10 10
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Shotgun Sequencing 1995-2006
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“classical” Sequencing 1995-2006
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Deep Sequencing New fast and cheap methods for sequencing Replacing ? ‘classical’ Sanger sequencing (covered if time allows…)
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The level of resolution: the ‘basic unit’ example DNA Is genome is the “largest unit” ? 2008: MetaGenomics The BIOME project : A community of genomes in human body
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SEARCH for numbers… How many nucleotides in chromosome 7 of human…. 1.Search “Google like” 2.Search “PubMED like” 3. Your way HM3: the value, the source
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The SOLUTION Dedicated resources (=Databases) that are focused for the genome ‘building blocks’ 1.NCBI 2.EBI 3. more… Centralized Achieve for DB, Tools, Protocols, Books, Drugs, education etc
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