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Workshop in Bioinformatics 2009

Workshop in Bioinformatics 2009. Class 2. Michal Linial Room A-515 michall@cc.huji.ac.il. Workshop in Bioinformatics (2). Bioinformatics is the computer-assisted data management discipline :

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Workshop in Bioinformatics 2009

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  1. Workshop in Bioinformatics2009 Class 2 Michal Linial Room A-515 michall@cc.huji.ac.il

  2. Workshop in Bioinformatics (2) Bioinformatics is the computer-assisted data management discipline : Gather, store, analyze, integrate biological and genetic information (data), and represent this information efficiently.

  3. Bioinformatics - two faces • Analysis and interpretation of various types of data (sequences nt, aa, domains, signatures, structures, RNAs) • Development of new algorithms / statistics to assess biological information • Development and implementation of tools for access and management different types of information (DB, Models, Maps..)

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

  5. What do you mean by “data”… Raw (primary) Data Sequences RNA DNA Genome Variations SNP Mutations

  6. 3’ Template G C A T G C 5’ 5’ Primer dATP dCTP dGTP dTTP ddCTP dATP dCTP dGTP dTTP ddTTP dATP dCTP dGTP dTTP ddATP dATP dCTP dGTP dTTP ddGTP GddC GCddA GCAddT ddG GCATGddC GCATddG DNA Sequencing “Classical” (Sanger)

  7. G T short _ _ C A G C A T G C + + long capillary unit New technology “454” technology (not in this class) ABI 3700 96x700 bases

  8. What do you mean data… Raw (primary) Data Sequences RNA DNA Genome Variations SNP Mutations

  9. Shotgun Sequencing Isolate Chromosome ShearDNA into Fragments Clone into Seq. Vectors Sequence

  10. Shotgun Sequencing Assembled Sequence Sequence Chromatogram Send to Computer

  11. Rat Sequencing

  12. Deep Sequencing New fast and cheap methods for sequencing Replacing ? ‘classical’ Sanger sequencing (not covered in this class but introduced later)

  13. The main topics • Introduction to databases • Working with sequences / Pairwise comparison • Database similarity searching • Profile building and searching • Functional resources • Genomics • Proteomics • Integrative resources • Introduction to systems biology • More…

  14. The goal of the course • Introduction to variety of databases and tools • Independence in working with available resources • Critical evaluation of web tools • Exposure to the main needs of modern biologist • Leverage your research skills • Discussing key issues in “new biology” • Presenting front-line research projects based on BI ….but mainly fun

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