Copyright OpenHelix. No use or reproduction without express written consent1

WormBase Genetics, genomics, and biology resource of C. elegans and related nematodes Materials prepared by: Cynthia Perreault-Micale, Ph.D. Jennifer Williams, Ph.D. Updated: Q Version 2

WormBase Agenda Introduction and Credits Basic Search and Gene Display Genome Browser Sequence Searches WormMart Tool Searching SNPs, Markers, and Strains Summary Exercises Copyright OpenHelix. No use or reproduction without express written consent3

WormBase Introduction Copyright OpenHelix. No use or reproduction without express written consent4 WormBase content is updated regularly

WormBase Credits Team: National Human Genome Research Institute: British Medical Research Council: Copyright OpenHelix. No use or reproduction without express written consent5 “Founded in 2000, the WormBase Consortium is led by Paul Sternberg of CalTech, Richard Durbin of the Wellcome Trust Sanger Institute, Lincoln Stein of Cold Spring Harbor and John Spieth of the Washington University Genome Sequencing Center.” WormBase is supported by a grant from the National Human Genome Research Institute at the US National Institutes of Health # P41 HG02223 and the British Medical Research Council.

WormBase Data Content – Community Participation Copyright OpenHelix. No use or reproduction without express written consent6

WormBase Publications WormBook: NAR: Copyright OpenHelix. No use or reproduction without express written consent7

WormBase User Guide Copyright OpenHelix. No use or reproduction without express written consent8

WormBase Agenda Introduction and Credits Basic Search and Gene Display Genome Browser Sequence Searches WormMart Tool Searching SNPs, Markers, and Strains Summary Exercises Copyright OpenHelix. No use or reproduction without express written consent9

Basic Searches Choose search category from drop-down menu Enter keyword in query box Select applicable boxes Click “Search” Copyright OpenHelix. No use or reproduction without express written consent10 Keyword Category Search

sqt-3 Sample Search for sqt-3 Sample search: Anything; sqt-3; unclick Wormbase Suggest Click on any result to see more detailed information Copyright OpenHelix. No use or reproduction without express written consent11 Select # of hits Search

Gene Summary Display Overview sqt-3 overview Various categories Closer look at sections next Copyright OpenHelix. No use or reproduction without express written consent related data genomic location expression function identification gene ontology genetics homology reagents literature 12

Gene Display: Identification Info Copyright OpenHelix. No use or reproduction without express written consent13 Approved gene name Sequenc e name Aliases WormBase Gene ID orthology Click ‘+’ to display additional sequences

Gene Display: Genetic Location 14 Genetic Map Position Copyright OpenHelix. No use or reproduction without express written consent Genomic Position

Gene Display: Expression Copyright OpenHelix. No use or reproduction without express written consent15

Gene Display: Function Copyright OpenHelix. No use or reproduction without express written consent16 Click ‘+’ to expand tables Top Lower

Gene Display: Gene Ontology & Genetics Copyright OpenHelix. No use or reproduction without express written consent17 Link to evidence code definitions

Gene Display: Homology Copyright OpenHelix. No use or reproduction without express written consent18 Click here for pairwise orthologies Click here for phylogenetic trees

Gene Display: Reagents & Bibliography Copyright OpenHelix. No use or reproduction without express written consent19

Basic Literature Search From Homepage Copyright OpenHelix. No use or reproduction without express written consent20 osm-9 Basic & Advanced options Our example: Keyword - osm-9 gene Annotated with disease (all) terms Other options as default

Basic Literature Search Results Copyright OpenHelix. No use or reproduction without express written consent21 Toggle open sections Options Full tutorial

WormBase Agenda Introduction and Credits Basic Search and Gene Display Genome Browser Sequence Searches WormMart Tool Searching SNPs, Markers, and Strains Summary Exercises Copyright OpenHelix. No use or reproduction without express written consent22

Specialized Searches Browse C. elegans and other genomes using the Genome search option Search for sequences in protein, genomic DNA and EST databases with Blast/Blat WormMart provides easy access to diverse categorized data Markers aids mapping experiments by finding SNPs & visible genetic markers Genetic Maps allows examination of entire chromosomes at various levels of detail Copyright OpenHelix. No use or reproduction without express written consent23 Select

Genome Browser Copyright OpenHelix. No use or reproduction without express written consent 24 Click here Suite of tools for further analysis, see improvements

Overview of Search Results Copyright OpenHelix. No use or reproduction without express written consent25 Genomic Region shown in top three sections Overview, Region and Details panels Data Tracks – annotations you can customize Display Settings & Add your own tracks Closer look at sections next Display Settings & Add your own tracks Data Tracks Detail Panel Region Panel Overview Panel

Basic Features of the Three Panels Copyright OpenHelix. No use or reproduction without express written consent26 Genetic markers Sequence 10X vs. Details Show, hide, share or change tracks Mouse-over or click

Navigation Methods Copyright OpenHelix. No use or reproduction without express written consent27 Navigate from here using Scroll/Zoom & dropdown Rubber band navigation from any rulers Click on rulers & drag to select region

Data Tracks Copyright OpenHelix. No use or reproduction without express written consent28 Click here Check boxes to turn tracks all on or all off Or add individual track New Track Drag this to top New track & new order Drag to re-order tracks vertically

Configuring your Tracks Copyright OpenHelix. No use or reproduction without express written consent29 Select Configure tracks to open Track Options

More Browser Options Copyright OpenHelix. No use or reproduction without express written consent30 Display Settings & Add your own tracks are at the end of the results page Display Settings & Add your own tracks

WormBase Agenda Introduction and Credits Basic Search and Gene Display Genome Browser Sequence Searches WormMart Tool Searching SNPs, Markers, and Strains Summary Exercises Copyright OpenHelix. No use or reproduction without express written consent31

Sequence Searches Copyright OpenHelix. No use or reproduction without express written consent32 Click here to Search Choose to search a protein or nucleotide database Click Here Choose database to search

Sequence Search Results Copyright OpenHelix. No use or reproduction without express written consent33 Click Here

WormBase Agenda Introduction and Credits Basic Search and Gene Display Genome Browser Sequence Searches WormMart Tool Searching SNPs, Markers, and Strains Summary Exercises Copyright OpenHelix. No use or reproduction without express written consent34

WormMart Copyright OpenHelix. No use or reproduction without express written consent35 Click here for WormMart Search

WormMart Background Copyright OpenHelix. No use or reproduction without express written consent36

A Basic WormMart Search Copyright OpenHelix. No use or reproduction without express written consent37 Click WormMart’s 3 Simple Steps: 1.Select data 2.Select filters & attributes 3.Select results display

Selecting Filters Copyright OpenHelix. No use or reproduction without express written consent38 Click on any + to expand filter category Click here

Selecting Search Criteria Copyright OpenHelix. No use or reproduction without express written consent39 Select Men u Scroll to Scroll bar

Accessing Results Copyright OpenHelix. No use or reproduction without express written consent40 Click

Results Page Copyright OpenHelix. No use or reproduction without express written consent41

Customizing Your Results - Attributes Copyright OpenHelix. No use or reproduction without express written consent42

WormBase Agenda Introduction and Credits Basic Search and Gene Display Genome Browser Sequence Searches WormMart Tool Searching SNPs, Markers, and Strains Summary Exercises Copyright OpenHelix. No use or reproduction without express written consent43

SNPs, Markers and Strains Search Copyright OpenHelix. No use or reproduction without express written consent44 SNPs, Markers and Strains

SNPs, Markers and Strains Search Form Copyright OpenHelix. No use or reproduction without express written consent45 Click Here

Graphic Search Results Copyright OpenHelix. No use or reproduction without express written consent46 fog-2

Tabular Search Results & Links Copyright OpenHelix. No use or reproduction without express written consent47 Listed in order of position

WormBase Agenda Introduction and Credits Basic Search and Gene Display Genome Browser Sequence Searches WormMart Tool Searching SNPs, Markers, and Strains Summary Exercises Copyright OpenHelix. No use or reproduction without express written consent48

Summary of WormBase Extensive Gene Summary Page Copyright OpenHelix. No use or reproduction without express written consent49 Many Search Options Powerful Genome Browser

Comprehensive Copyright OpenHelix. No use or reproduction without express written consent50 WormMart Search for a sequence Display markers, SNPs & strains carrying SNPS

WormBase Agenda Introduction and Credits Basic Search and Gene Display Gene Summary Page Genome Browser Sequence Searches WormMart Tool Searching SNPs, Markers, and Strains Summary Exercises Copyright OpenHelix. No use or reproduction without express written consent51

Copyright OpenHelix. No use or reproduction without express written consent52