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

Slides:

Advertisements

Similar presentations

After 13 years of scientist work predominatly in USA & UK the DNA sequence of the human genome was completed in 2003 Any ideas how they did it? What would.

Advertisements

CZ5225 Methods in Computational Biology Lecture 9: Pharmacogenetics and individual variation of drug response CZ5225 Methods in Computational Biology.

Learning Evolution and Phylogeny Through Tree Building Larry Aaronson, Utica College David Treves, Indiana Univ., Southeast Monica Trifas, Jacksonville.

Phylogenetic Trees Understand the history and diversity of life. Systematics. –Study of biological diversity in evolutionary context. –Phylogeny is evolutionary.

Summer Bioinformatics Workshop 2008 Comparative Genomics and Phylogenetics Chi-Cheng Lin, Ph.D., Professor Department of Computer Science Winona State.

BIOINFORMATICS Ency Lee.

Introduction to Bioinformatics

Predicting the Function of Single Nucleotide Polymorphisms Corey Harada Advisor: Eleazar Eskin.

Analysis of Phenotypic Variations in the Mouse Genome Caused by Single Nucleotide Polymorphisms Corey Harada Advisor: Eleazar Eskin.

Integration of Bioinformatics into Inquiry Based Learning by Kathleen Gabric.

Evolutionary Genome Biology Gabor T. Marth, D.Sc. Department of Biology, Boston College Medical Genomics Course – Debrecen, Hungary, May 2006.

Determination of Sites of CYP1B1 Mutations in Aligned Sequences of Cytochrome P450 Family Members and 3D-Structural Model by: Betsabeh Khoramian Tusi.

Protein Evolution Jean Yeh, SoCalBSI Mike Thompson, UCLA Summer 2005.

1-month Practical Course Genome Analysis Lecture 3: Residue exchange matrices Centre for Integrative Bioinformatics VU (IBIVU) Vrije Universiteit Amsterdam.

BLOSUM Information Resources Algorithms in Computational Biology Spring 2006 Created by Itai Sharon.

Bioinformatics Unit 1: Data Bases and Alignments Lecture 3: “Homology” Searches and Sequence Alignments (cont.) The Mechanics of Alignments.

Arabidopsis Gene Project GK-12 April Workshop Karolyn Giang and Dr. Mulligan.

Multiple Sequence Alignments and Phylogeny.  Within a protein sequence, some regions will be more conserved than others. As more conserved,

Genes (3.1) IB Diploma Biology Essential Idea: Heritable traits are passed down to offspring through genes.

Evolution Chapters Evolution is both Factual and the basis of broader theory What does this mean? What are some factual examples of evolution?

Statistical Tool for Identifying Sequence Variations That Correlate with Virus Phenotypic Characteristics in the Virus Pathogen Resource (ViPR) July 22,

8.7 – Mutations. Key Concept  Mutations are changes in DNA that may or may not affect phenotype. mutated base.

SNP Haplotypes as Diagnostic Markers Shrish Tiwari CCMB, Hyderabad.

Development and Application of SNP markers in Genome of shrimp (Fenneropenaeus chinensis) Jianyong Zhang Marine Biology.

1 Gene – Expression – Mutation - polymorphism. 2 How are genes expressed ? Nucleus Cytoplasm DNA Transcription Poly(A ) Cap Pre-mRNA Splicing Cap Poly(A)

Next-Generation Sequencing Eric Jorgenson Epidemiology 217 2/28/12.

Sequence Alignment Csc 487/687 Computing for bioinformatics.

BLAST: Basic Local Alignment Search Tool Altschul et al. J. Mol Bio CS 466 Saurabh Sinha.

Basic Local Alignment Search Tool BLAST Why Use BLAST?

Lecture 6. Functional Genomics: DNA microarrays and re-sequencing individual genomes by hybridization.

Hepatitis C Analysis of Sequence Data from ARUP and NCBI databases By Ian Odell.

Human Genomics. Writing in RED indicates the SQA outcomes. Writing in BLACK explains these outcomes in depth.

Examining the Genetic Similarity and Difference of the Three Progressor Groups at the First and Middle Visits Nicole Anguiano BIOL398: Bioinformatics Laboratory.

Sequence Alignment Abhishek Niroula Department of Experimental Medical Science Lund University

Mutations in DNA changes in the DNA sequence that can be inherited can have negative effects (a faulty gene for a trans- membrane protein leads to cystic.

Chapter 2 Genetic Variations. Introduction The human genome contains variations in base sequence from one individual to another. Some sequence variants.

Evolutionary Genome Biology Gabor T. Marth, D.Sc. Department of Biology, Boston College

Examining Genetic Similarity and Difference of the Three Progressor Groups at the First and Middle Visits Nicole Anguiano BIOL398: Bioinformatics Laboratory.

Determining Sequence Relationships

Mutation. What you need to know How alteration of chromosome number or structurally altered chromosomes can cause genetic disorders How point mutations.

Research Paper on BioInformatics

MOLECULAR GENETICS Mutations Definition

Variation among organisms

Gene Mutations.

Genes (3.1) Essential Idea: Heritable traits are passed down to offspring through genes.

Pipelines for Computational Analysis (Bioinformatics)

Sequence Alignments—part 2

Types of Mutations.

School of Pharmacy, University of Nizwa

DNA and mutations SC.912.L.16.4.

Types of Mutations Thanks to Ms. Sara Dozier and Ms. Kimball for many of these slides! *

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Mutations changes in the DNA sequence that can be inherited

Mutations & Genetic Engineering

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

ICAR-Directorate of Foot-and-mouth disease, Mukteswar, India

Relationship between Genotype and Phenotype

Mutations Any change in an organism’s DNA. Mutations in somatic cells only impact individual; mutations in gametes may impact offspring. 2 Types: A. Gene.

Basic Local Alignment Search Tool

Explore Evolution: Instrument for Analysis

A. Papa, K. Dumaidi, F. Franzidou, A. Antoniadis

School of Pharmacy, University of Nizwa

Figure 3 Stepwise strategy of bioinformatic analysis of sequencing results We obtained 7,292,715 and 303,698 DNA sequence reads from the affected brain.

Unit Genomic sequencing

Mutation Notes.

Section 20.4 Mutations and Genetic Variation

Phylogenetic analysis and amino acid sequences comparison of HO endonucleases. Phylogenetic analysis and amino acid sequences comparison of HO endonucleases.

Nonsense and missense amino acid mutation analysis.

Comparison of the predicted amino acid sequences of murine Rin (GenBank accession number U71202), human Rin (U71204), murine Rit (U71205), human Rit (U71203),

Presentation transcript:

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  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 similarity between 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: LabelIDAccession No.Length Revision dateCountry/Source 1.TWHAp AUG-2003Taiwan: patient #01 TWC2Ay AUG-2003Taiwan: Hoping Hospital 2.TWC3Ay AUG-2003Taiwan: Hoping Hospital 3.TWKAp AUG-2003Taiwan: patient #06 4.TWSAp AUG-2003Taiwan: patient #04 5.TWYAp AUG-2003Taiwan: patient #02 6.UrbaniAy AUG-2003USA: Atlanta 7.TWJAp AUG-2003Taiwan: patient #043 8.TWCAy JUN-2003Taiwan, first fatal case

Finding structural similarity

SNPs identified

Density distribution of polymorphisms

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.

Side by Side Comparison of Trees

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

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