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An analysis of “Bioinformatics analysis of SARS coronavirus genome polymorphism” by Pavlović-Lažetić, et. al
Angela BrooksJuly 9, 2004SoCalBSI Article Presentation
Outline
Background Purpose Experimental Methods Results Conclusions Possible Future Studies Importance of the work to society
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 similaritybetween isolates to determine the phylogeny of the
SARS-CoV isolates
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
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
2 Step Sequence Comparisons
1. Structurally Identical Parts
Identify regions of insertions and deletions with a reference set
2. SNPs in Structurally Identical Parts
From regions in Part 1, find SNPs in those regions
2 Step Sequence Comparisons
1. Structurally Identical Parts Similar to sequence
alignment
2. SNPs in Structurally Identical Parts
Reference Set (database)
Other isolate sequences (queries)
How were sequences obtained?
Our old friend NCBI:Label ID Accession No. Length Revision date Country/Source
1. TWH Ap006557.1 29727 02-AUG-2003 Taiwan: patient #01
TWC2 Ay362698.1 13-AUG-2003 Taiwan: Hoping Hospital
2. TWC3 Ay362699.1 29727 13-AUG-2003 Taiwan: Hoping Hospital
3. TWK Ap006559.1 29727 02-AUG-2003 Taiwan: patient #06
4. TWS Ap006560.1 29727 02-AUG-2003 Taiwan: patient #04
5. TWY Ap006561.1 29727 02-AUG-2003 Taiwan: patient #02
6. Urbani Ay278741.1 29727 12-AUG-2003 USA: Atlanta
7. TWJ Ap006558.1 29725 02-AUG-2003 Taiwan: patient #043
8. TWC Ay321118.1 29725 26-JUN-2003 Taiwan, first fatal case
Qualitative Analysis of Sequence Variation
Based on structural similarity and SNPs, a tree was constructed to show sequence divergence
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.
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