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Angela Brooks July 9, 2004 SoCalBSI Article Presentation

An analysis of “Bioinformatics analysis of SARS coronavirus genome polymorphism” by Pavlović-Lažetić, et. al. Angela Brooks July 9, 2004 SoCalBSI Article Presentation. Outline. Background Purpose Experimental Methods Results Conclusions Possible Future Studies

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Angela Brooks July 9, 2004 SoCalBSI Article Presentation

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  1. An analysis of “Bioinformatics analysis of SARS coronavirus genome polymorphism” by Pavlović-Lažetić, et. al Angela Brooks July 9, 2004 SoCalBSI Article Presentation

  2. Outline • Background • Purpose • Experimental Methods • Results • Conclusions • Possible Future Studies • Importance of the work to society

  3. Background • The authors analyzed the genomes of 38 isolates of the Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) • Isolates: virus “strains” that are apart/cut off from one another by location • Looking for: • single nucleotide polymorphisms(SNPs) • insertions and deletions • sequence similarity between isolates to determine the phylogeny of the SARS-CoV isolates

  4. SNPs – Single Nucleotide Polymorphisms • A single point mutation in the genome • Types of mutations caused by SNPs: • Silent • no change • Missense • AA change in protein product • Nonsense • Change AA to “stop” • Other • Change in other functional/regulatory region ...ATCGATGC... ...ATCGTTGC... T

  5. Purpose of Paper • Establish the origin of the virus. • Find regions in genome with high levels of sequence polymorphisms • Discover the evolutionary path of the virus • lead towards preventing or curing the disease that it causes

  6. Structurally Identical Parts Identify regions of insertions and deletions with a reference set SNPs in Structurally Identical Parts From regions in Part 1, find SNPs in those regions 2 Step Sequence Comparisons

  7. Structurally Identical Parts Similar to sequence alignment SNPs in Structurally Identical Parts Reference Set (database) Other isolate sequences (queries) 2 Step Sequence Comparisons

  8. How were sequences obtained? • Our old friend NCBI:

  9. Finding structural similarity

  10. SNPs identified

  11. Density distribution of polymorphisms

  12. Qualitative Analysis of Sequence Variation • Based on structural similarity and SNPs, a tree was constructed to show sequence divergence

  13. ClustalW used as a control for tree • ClustalW with PhyloDraw was used to draw a tree for comparison with “homemade” tree • ZMY1 and ZJ01 are distant from representative group.

  14. Side by Side Comparison of Trees

  15. New Problems to Address • Not much analysis was done on results from study • i.e. Found SNPs and structurally similar regions but not significant without analysis • What could be analyzed further? • Examine regions of conservation for functional importance • Examine phenotypic affect of amino acid mutation • For isolates in a similar group, compare phenotypic characteristics to genotypic similarites • Uncover phenotypic/genotypic relationships

  16. Why is SARS-CoV research important? • Previous year’s “outbreak” uncovered in China • Anxiety over viruses • Possible bioterrorism • Understanding SARS-CoV may help to understand similar virus

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