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Welcome to Introduction to Bioinformatics Monday, 7 March 2005

Welcome to Introduction to Bioinformatics Monday, 7 March 2005. Genome Identification. Polymerase Chain Reaction (PCR) Phylogenetic trees Discovery Question 29 (West Nile Virus time course). Polymerase Chain Reaction (PCR). Problem:. Need DNA sequence for comparisons.

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Welcome to Introduction to Bioinformatics Monday, 7 March 2005

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  1. Welcome toIntroduction to BioinformaticsMonday, 7 March 2005 Genome Identification • Polymerase Chain Reaction (PCR) • Phylogenetic trees • Discovery Question 29 (West Nile Virus time course)

  2. Polymerase Chain Reaction (PCR) Problem: • Need DNA sequence for comparisons • Sequencing entire genome impractical • Single gene tiny fraction of whole

  3. Polymerase Chain Reaction (PCR) Animation (requires Shockwave): http://www.dnalc.org/shockwave/pcranwhole.html Static explanation: http://allserv.rug.ac.be/~avierstr/principles/pcr.html

  4. Polymerase Chain Reaction (PCR) primer primer Target Sequence Primer sequences must be highly conserved

  5. Polymerase Chain Reaction (PCR) primer primer Target Sequence Primer sequences must be highly conserved How to choose a target?

  6. intergenicregions genes proteins Polymerase Chain Reaction (PCR) How to choose a target? Rapid change Slow change conserved proteins

  7. genes proteins Polymerase Chain Reaction (PCR) How to choose a target? Rapid change Slow change intergenicregions conserved proteins genes proteins Ribosome

  8. conserved RNAs Polymerase Chain Reaction (PCR) How to choose a target? Rapid change Slow change intergenicregions conserved proteins genes proteins Ribosomal protein Ribosomal RNA

  9. Phylogenetic TreesCyanobacterial tree using 16S rRNA • Collect 16S rRNA sequences • Crop sequences  core • Pairwise comparisons • Collect pairwise distances • Construct tree from distances

  10. Phylogenetic TreesCyanobacterial tree using 16S rRNA Do it!

  11. Phylogenetic TreesCyanobacterial tree using 16S rRNA

  12. Phylogenetic TreesCyanobacterial tree using 16S rRNA

  13. Phylogenetic TreesCyanobacterial tree using 16S rRNA

  14. Phylogenetic TreesCyanobacterial tree using 16S rRNA

  15. Phylogenetic TreesCyanobacterial tree using 16S rRNA Anabaena PCC 7120 Anabaena variabilies Nostoc punctiforme Crocosphaera Trichodesmium Synechococcus PCC 7942 Synechocystis PCC 6803 Gloeobacter Thermosynechococcus Prochlorococcus MED4 Prochlorococcus SS120 Prochlorococcus MIT9313 Synechococcus WH8102

  16. Coming Attractions Problem Set on Chapter 2 • Use Blast scores to recreate nucleus analysis of Shinozawa • T-test of results • Tree manufacture New BioLingua Feature • Alignments • Tables

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