Copyright OpenHelix. No use or reproduction without express written consent1

VBRC: Viral Bioinformatics Resource Center Viral Data & Analysis Tools Materials prepared by: Cynthia Perreault-Micale, Ph.D. Updated: Q Version 1.0_0609

Copyright OpenHelix. No use or reproduction without express written consent3 VBRC Agenda Introduction and Credits VBRC Resources Virus Orthologous Clusters (VOCs) VOCs Additional Features Additional Tools Summary Exercises VBRC:

VBRC Homepage Copyright OpenHelix. No use or reproduction without express written consent4

VBRC Credits Copyright OpenHelix. No use or reproduction without express written consent5

News, Publications & More Homepage top navigation menu Copyright OpenHelix. No use or reproduction without express written consent6

A Variety of Analytical Tools & Resources Copyright OpenHelix. No use or reproduction without express written consent7 Contact

An Example Copyright OpenHelix. No use or reproduction without express written consent8 VBRC offers many resources & tools This shows genes common to 2 viral genomes From Graphical Ortholog Synteny Comparison tool A comprehensive database of viral information

Copyright OpenHelix. No use or reproduction without express written consent9 VBRC Agenda Introduction and Credits VBRC Resources Virus Orthologous Clusters (VOCs) VOCs Additional Features Additional Tools Summary Exercises VBRC:

To Access VBRC Resources: Copyright OpenHelix. No use or reproduction without express written consent10 Select data or analysis Click

Virus Descriptions Copyright OpenHelix. No use or reproduction without express written consent11 Click Help

Descriptions Copyright OpenHelix. No use or reproduction without express written consent12 Blog Posts General info & links Analysis tools Specific info & details

Available Genomes Copyright OpenHelix. No use or reproduction without express written consent13 Click here Or click here

Genome List Copyright OpenHelix. No use or reproduction without express written consent14 Click

Locating Strain-Specific Genome Information Copyright OpenHelix. No use or reproduction without express written consent15 Click

Strain-Specific Details, Links & Options Copyright OpenHelix. No use or reproduction without express written consent16 Click Options Download a genome in FASTA format or Zip archive Send to view in the Viral Genome Organizer browser

Homepage Data Tab – Sequence Section Copyright OpenHelix. No use or reproduction without express written consent17 Search for genes by name, position, weight, motif, PDB ID and more

Homepage Data Tab – Annotation Section Copyright OpenHelix. No use or reproduction without express written consent18

Analytical Tools Copyright OpenHelix. No use or reproduction without express written consent19 Or click here Click here

Similarity Searches Copyright OpenHelix. No use or reproduction without express written consent20 The major difference is how the alignment data are displayed Our focus is XS BLAST List format - scores at top, alignments below User-friendly format

XS BLAST Search Copyright OpenHelix. No use or reproduction without express written consent21 Click Enter here Click

XS BLAST Search Options & Example Copyright OpenHelix. No use or reproduction without express written consent22 Input sequence Click Link to help - green icons

XS BLAST Search Results Copyright OpenHelix. No use or reproduction without express written consent23 Details of your search We will enlarge & examine the results table next

XS BLAST Search Results Table Copyright OpenHelix. No use or reproduction without express written consent24

XS BLAST Search Results Table – Part 2 Copyright OpenHelix. No use or reproduction without express written consent25

Accessing the Ortholog Comparison Tools Copyright OpenHelix. No use or reproduction without express written consent26 Click here

Ortholog Comparison Tools Copyright OpenHelix. No use or reproduction without express written consent27 Click 3 Ortholog Comparison tools are available Pairwise & Multi-genome Ortholog Comparison tools function similarly to display lists of genes shared or missing between genomes Graphical Ortholog Synteny data are graphical

Pairwise Ortholog Comparisons Copyright OpenHelix. No use or reproduction without express written consent28

Pairwise Ortholog Comparison Search Results Copyright OpenHelix. No use or reproduction without express written consent29

Click Graphical Ortholog Synteny Comparisons Copyright OpenHelix. No use or reproduction without express written consent30

Graphical Results Copyright OpenHelix. No use or reproduction without express written consent31 Genomes shown on x & y axes Dark & light blue marks show genes present on + or – strands, respectively Red & green marks show genes that align on opposing strands Black dots are for genes present in only one genome Key

Copyright OpenHelix. No use or reproduction without express written consent32 VBRC Agenda Introduction and Credits VBRC Resources Virus Orthologous Clusters (VOCs) VOCs Additional Features Additional Tools Summary Exercises VBRC:

Accessing Viral Orthologous Clusters (VOCs) Copyright OpenHelix. No use or reproduction without express written consent33 Click here Or click here Or here

VBRC Tools Copyright OpenHelix. No use or reproduction without express written consent34

VOCs Copyright OpenHelix. No use or reproduction without express written consent35 Click Help Java-based tool to search & extract genome, gene & protein data from VBRC Frequently updated, latest is PDB Scan

Viral Orthologous Clusters (VOCs) - Basics Copyright OpenHelix. No use or reproduction without express written consent36 Click First choose a database An empty VOCs search will open We will review filter tabs next Search options Filters

VOCs: Sequence Filter – Top Section Copyright OpenHelix. No use or reproduction without express written consent37

VOCs: Sequence Filter – Lower Section Copyright OpenHelix. No use or reproduction without express written consent38 Click

VOCs: Sequence Filter – DNA Constraints Copyright OpenHelix. No use or reproduction without express written consent39 This option works the same as the Amino Acid Constraints

VOCs: Ortholog Group Filter – Top Section Copyright OpenHelix. No use or reproduction without express written consent40 Top dropdown menus to select virus & gene of interest Use Ortholog Group Selector if you know something about the ortholog group you are searching for, i.e. ID or name

VOCs: Ortholog Group Filter – Lower Section Copyright OpenHelix. No use or reproduction without express written consent41 Select Click

VOCs: Genome Filter & Virus Selector Copyright OpenHelix. No use or reproduction without express written consent42 Click Final constraint tool

VOCs: Example Criteria Copyright OpenHelix. No use or reproduction without express written consent43 Click Our example: all Poxviridae genes within ortholog group 'Thymidine kinase' Scrol l

VOCs: Applying Constraints with Toolbar Buttons Copyright OpenHelix. No use or reproduction without express written consent44 Click

VOCs: Gene Results Table Copyright OpenHelix. No use or reproduction without express written consent45 You can highlight one or more gene entries and click on 'Display' to find out more about it Click

VOCs: Gene Data & Gene Notes Tabs Copyright OpenHelix. No use or reproduction without express written consent46 We will examine the 'DNA/aa Statistics' tab in the next slide

VOCs: DNA/aa Statistics Tab Copyright OpenHelix. No use or reproduction without express written consent47 Top Section Middle Section Lower Section

VOCs: 'Family' Button Copyright OpenHelix. No use or reproduction without express written consent48 Click This will display all genes that fall into the same Ortholog Group

VOCs: 'Sequences' Button Copyright OpenHelix. No use or reproduction without express written consent49 Click This will show color-coded DNA & protein sequences for the highlighted gene

VOCs: 'Notes' Button Copyright OpenHelix. No use or reproduction without express written consent50 Click This will open the same notes information as you find in the gene information table

Copyright OpenHelix. No use or reproduction without express written consent51 VBRC Agenda Introduction and Credits VBRC Resources Virus Orthologous Clusters (VOCs) VOCs Additional Features Additional Tools Summary Exercises VBRC:

VOCs: Column Options Copyright OpenHelix. No use or reproduction without express written consent52 Click

VOCs: GO Terms & InterPro Hits Copyright OpenHelix. No use or reproduction without express written consent53 Click

VOCs: PDB Structures Copyright OpenHelix. No use or reproduction without express written consent54 Click Enter Family & Dates

VOCs: Sequence Searcher Copyright OpenHelix. No use or reproduction without express written consent55 Click

VOCs: Sequence Searcher – Input Options Copyright OpenHelix. No use or reproduction without express written consent56 Click

VOCs: Sequence Searcher - Results Copyright OpenHelix. No use or reproduction without express written consent57

VOCs: Blast Copyright OpenHelix. No use or reproduction without express written consent58Copyright OpenHelix. No use or reproduction without express written consent58Copyright OpenHelix. No use or reproduction without express written consent58 Click

VOCs: Alignment CLICK Copyright OpenHelix. No use or reproduction without express written consent59

Base by Base Alignment Editor Copyright OpenHelix. No use or reproduction without express written consent60 Click Drag Click Color-coded bases & interactive sequences Results

Base by Base Alignment Editor – Menu Options Copyright OpenHelix. No use or reproduction without express written consent61

VOCs: Analysis Tools - Hydrophobicity Plot Copyright OpenHelix. No use or reproduction without express written consent62 Click

VOCs: Analysis Tools - DNA Grapher Copyright OpenHelix. No use or reproduction without express written consent63 Click

VOCs: JDotter Copyright OpenHelix. No use or reproduction without express written consent64 Click

Copyright OpenHelix. No use or reproduction without express written consent65 VBRC Agenda Introduction and Credits VBRC Resources Virus Orthologous Clusters (VOCs) VOCs Additional Features Additional Tools Summary Exercises VBRC:

Viral Genome Organizer (VGO) Copyright OpenHelix. No use or reproduction without express written consent66 JAVA-based, displays genome information such as genes, ORFs & start/stop codons

Genome Annotation Transfer Utility (GATU) Copyright OpenHelix. No use or reproduction without express written consent67 For genomes not as well characterized BLAST vs. a reference genome to add annotation eGATU – 'easy GATU', no reference needed

Genome-Based Fingerprint Scanning (GFS) Copyright OpenHelix. No use or reproduction without express written consent68 Identify proteins in genomes not well characterized from mass spectrometry data Comparison to a reference genome Easy & inexpensive method to identify proteins

Copyright OpenHelix. No use or reproduction without express written consent69 VBRC Agenda Introduction and Credits VBRC Resources Virus Orthologous Clusters (VOCs) VOCs Additional Features Additional Tools Summary Exercises VBRC:

Comprehensive, Updated & Freely Available Data Copyright OpenHelix. No use or reproduction without express written consent70 Curated sequence data Many resources & tools NIH/NIAID Category A, B & C priority pathogens

Copyright OpenHelix. No use or reproduction without express written consent71 VBRC Agenda Introduction and Credits VBRC Resources Virus Orthologous Clusters (VOCs) VOCs Additional Features Additional Tools Summary Exercises VBRC:

Copyright OpenHelix. No use or reproduction without express written consent72