Copyright OpenHelix. No use or reproduction without express written consent1
NCBI Viral Genomes The NCBI Viral Genomes Resource Materials prepared by: Jennifer Williams, Ph.D. Updated: Q Version 2.0
Copyright OpenHelix. No use or reproduction without express written consent3 NCBI Viral Genomes Agenda Introduction & Credits Basic Search Tools: BLAST & PASC Tools: Protein Clusters Other Features Summary Exercises NCBI Viral Genomes:
Copyright OpenHelix. No use or reproduction without express written consent4 Introduction NCBI Viral Genomes Part of the NCBI Entrez-Genome collection Establishes a reference sequence for each viral genome Organizes data by taxonomy Provides tools to compare & analyze viral sequences Integrated with NCBI’s other databases
Copyright OpenHelix. No use or reproduction without express written consent5 The Discovery of Viruses still toxic FILTER removes bacteria Dimitri Ivanovski diseased tobacco leaves Martinus Beijerinck tobacco mosaic virus agent = poison “VIRUS” ( Latin )
Copyright OpenHelix. No use or reproduction without express written consent6 The Importance of Viruses MEDICAL AIDS Ebola Cancer Influenza Bio-terrorism AGRICULTURAL Wheat Mosaic Corn Necrosis Soybean Mosaic Tomato Wilt Agri-terrorism A virus infects a host cell. Replicates its genome & coat. Then breaks free to infect new cells.
Copyright OpenHelix. No use or reproduction without express written consent7 Managing Viral Genome Sequences HIV-1 250,000+ records... Reference Sequence NC_ reduced to one Reference Sequence Viral Sequences NCBI Viral Genomes
Copyright OpenHelix. No use or reproduction without express written consent8 NCBI Viral Genomes Preview Taxonomy RefSeq Genome Summary GenBank PubMed
Copyright OpenHelix. No use or reproduction without express written consent9 NCBI Viral Genomes Homepage Navigation
Copyright OpenHelix. No use or reproduction without express written consent10 NCBI Viral Genomes Agenda Introduction & Credits Basic Search Tools: BLAST & PASC Tools: Protein Clusters Other Features Summary Exercises NCBI Viral Genomes:
Copyright OpenHelix. No use or reproduction without express written consent11 Search for a Virus: Complete List of Genomes Scroll down Sort genomes by:Filter by host Download
Copyright OpenHelix. No use or reproduction without express written consent12 Search for a Virus: via Taxonomy Pick-list Select taxon
13 Search for a Virus: via Entrez-Genome Apple chlorotic leaf spot virus Search Results Overview display Genome sequences for all viruses in taxon Copyright OpenHelix. No use or reproduction without express written consent
14 Measles Virus Click Genome name RefSeq accession ID LengthProteins Genome neighbors Host & dates Source Copyright OpenHelix. No use or reproduction without express written consent
Nucleotides 15 Measles Virus: Taxonomy Structure PubMed Central Copyright OpenHelix. No use or reproduction without express written consent
16 Measles Virus: Accession ID GenBank Click Overview display Entrez Gene Genome ProjectPubMed Sequence Viewer
Copyright OpenHelix. No use or reproduction without express written consent17 Measles Virus: Proteins Protein length histogram Entrez Protein Entrez Gene
Copyright OpenHelix. No use or reproduction without express written consent18 Measles Virus: Genome Neighbors Reference sequence Genome neighbors Sequence differences are color-coded Sequence difference histogram
Copyright OpenHelix. No use or reproduction without express written consent19 NCBI Viral Genomes Agenda Introduction & Credits Basic Search Tools: BLAST & PASC Tools: Protein Clusters Other Features Summary Exercises NCBI Viral Genomes:
Copyright OpenHelix. No use or reproduction without express written consent20 Viral Genomes Tools
Copyright OpenHelix. No use or reproduction without express written consent21 Full BLAST tutorial BLAST
Copyright OpenHelix. No use or reproduction without express written consent22 PASC - Pairwise Sequence Comparison
Copyright OpenHelix. No use or reproduction without express written consent23 Viral genomes used for PASC PASC: Families
Copyright OpenHelix. No use or reproduction without express written consent24 Percent Identity (0 to 100%) ~ 400 comparisons with ~ 58% identity Click on bar for details Highly similar viruses # Viral Comparisons Key PASC: Histogram for Alphaflexiviridae
PASC: Histogram Details Copyright OpenHelix. No use or reproduction without express written consent25
Copyright OpenHelix. No use or reproduction without express written consent26 NC_ TIP: completed viral genomes only! PASC: Upload a Viral Genome for Comparison
Copyright OpenHelix. No use or reproduction without express written consent27 Scroll down Input sequence shares ~ 46% PASC: Query Results
Copyright OpenHelix. No use or reproduction without express written consent28 Input sequence Best matches PASC: Top 15 Matches from Query % identity
Copyright OpenHelix. No use or reproduction without express written consent29 NCBI Viral Genomes Agenda Introduction & Credits Basic Search Tools: BLAST & PASC Tools: Protein Clusters Other Features Summary Exercises NCBI Viral Genomes:
Copyright OpenHelix. No use or reproduction without express written consent30 5 classes of viruses 4 resources 1 Protein Clusters Homepage Note
Copyright OpenHelix. No use or reproduction without express written consent31 ABCDEFGHIJABCDEFGHIJ VOG: Clusters List
Copyright OpenHelix. No use or reproduction without express written consent32 Click VOG: Clusters List: Adenoviridae
Copyright OpenHelix. No use or reproduction without express written consent33 VOG: Detail Page
Copyright OpenHelix. No use or reproduction without express written consent34 VOG: Function Resource 2
Copyright OpenHelix. No use or reproduction without express written consent35 Click VOG: Functional Categories
Copyright OpenHelix. No use or reproduction without express written consent36 Family # Proteins VOG function VOG: Function: Regulation of Cellular Metabolism
Copyright OpenHelix. No use or reproduction without express written consent37 3 VOG: CDD Resource
Copyright OpenHelix. No use or reproduction without express written consent38 Click to sort table VOG: CDD Results
Copyright OpenHelix. No use or reproduction without express written consent39 4 VOG: BLAST Resource
Copyright OpenHelix. No use or reproduction without express written consent Click VOG: BLAST Query
Copyright OpenHelix. No use or reproduction without express written consent41 VOG: BLAST Results
Copyright OpenHelix. No use or reproduction without express written consent Protein found Associated VOG Other VOG members Virus class VOG: Search From Protein Clusters Homepage VOG search box
Copyright OpenHelix. No use or reproduction without express written consent43 VOG: by Taxonomy Groups Click
Copyright OpenHelix. No use or reproduction without express written consent44 NCBI Viral Genomes Agenda NCBI Viral Genomes: Introduction & Credits Basic Search Tools: BLAST & PASC Tools: Protein Clusters Other Features Summary Exercises
Copyright OpenHelix. No use or reproduction without express written consent45 Homepage Navigation Bar
Copyright OpenHelix. No use or reproduction without express written consent46 Citation, FAQs & Help
Copyright OpenHelix. No use or reproduction without express written consent47 Select best matches virus A best matches virus B Genotyping Click on example
Copyright OpenHelix. No use or reproduction without express written consent48 Influenza Virus Resource
Copyright OpenHelix. No use or reproduction without express written consent49 SARS Resource
Copyright OpenHelix. No use or reproduction without express written consent50 Non-NCBI Virus Databases
Copyright OpenHelix. No use or reproduction without express written consent51 Related Sites
Copyright OpenHelix. No use or reproduction without express written consent52 NCBI Viral Genomes Agenda NCBI Viral Genomes: Introduction & Credits Basic Search Tools: BLAST & PASC Tools: Protein Clusters Other Features Summary Exercises
Copyright OpenHelix. No use or reproduction without express written consent53 1 Reference Sequence Thousands of Viral Sequences ~ 400,000 sequences for HIV-1 1 RefSeq (NC_001802) Raw Data Molecular Standard NCBI Viral Genomes: Reduces Complexity NCBI Viral Genomes
Copyright OpenHelix. No use or reproduction without express written consent54 Viral Genomes: Integrated with NCBI Resources Taxonomy RefSeq Genome Summary GenBank PubMed
Copyright OpenHelix. No use or reproduction without express written consent55 Compare virus identities Explore virus protein clusters Add your own data for analysis & comparison NCBI Viral Genomes: Tools
Copyright OpenHelix. No use or reproduction without express written consent56 Other NCBI virus-specific databases Non-NCBI virus databases History & photos of viruses NCBI Viral Genomes: Numerous Link-Outs
Copyright OpenHelix. No use or reproduction without express written consent57 NCBI Viral Genomes Agenda NCBI Viral Genomes: Introduction & Credits Basic Search Tools: BLAST & PASC Tools: Protein Clusters Other Features Summary Exercises
Copyright OpenHelix. No use or reproduction without express written consent58