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Workshop in Bioinformatics 2010 Class # 75321 Class 8 March 2010.

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Presentation on theme: "Workshop in Bioinformatics 2010 Class # 75321 Class 8 March 2010."— Presentation transcript:

1 Workshop in Bioinformatics 2010 Class # 75321 Class 8 March 2010

2 (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…)

3 What do you mean by “data”… Raw (primary) Processed (analyzed) Integrated (systems)

4 What do you mean “raw data”… Raw (primary) Data Sequences RNA (many types) DNA Genome Variations SNP Mutations Copy Number Variations (CNV)

5 What do you mean “raw data”… Rate - Raw (primary) Data HM1: Identify 2 areas with a similar (?) trend

6 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

7 The level of resolution: the ‘basic unit’ example DNA Nucleotide to Genome level Technology: DNA / RNA SEQUENCING Nucleotide level

8 DNA Sequencing “Classical” (Sanger)

9 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

10 ABI 3700 96x700 bases Scale: capillary tech RUNs New technology “454” technology (not in this class)

11 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

12 Shotgun Sequencing 1995-2006

13 “classical” Sequencing 1995-2006

14 Deep Sequencing New fast and cheap methods for sequencing Replacing ? ‘classical’ Sanger sequencing (covered if time allows…)

15 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

16 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

17 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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