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Ensembl Exercises

This page contains links to all the exercises and walkthroughs the Ensembl Outreach team have available. You can use these to construct coursebooks for specific courses. Please note that Ensembl training materials are distributed under a Creative Commons BY license – you are required to credit Ensembl with the creation of these materials if you use them.

Please note the release number in the ‘Updated’ column. Some exercises are made to older Ensembl/Ensembl Genomes versions (releases) and may not work on the current site, as they were made for a specific course and have not been updated since. Those labelled E are the Ensembl release and those labelled EG are the Ensembl Genomes release.

Our blog contains more information about how you can plan and teach your own Ensembl browser workshop, using these exercises.

Walkthroughs

Topic Species Updated Walkthrough
Human 104 Genome assemblies, genes and transcripts in Ensembl, Demo
Human 107 Genome assemblies, genes and transcripts in Ensembl, Demo
Beta Ensembl Beta - Wheat 111 Finding genomics data in Ensembl Beta, Demo
BioMart Barley (Hordeum vulgare) 104 Data export with BioMart
BioMart Chicken 111 Bulk export of data with BioMart, Demo
BioMart Fusarium solani (v2.0) 56 Exporting wheat gene data with BioMart, demo
BioMart Human 104 Bulk export of data with BioMart, Demo
BioMart Mosquito (Anopheles gambiae) 104 Exporting gene data with BioMart, demo
BioMart Rice (Oryza sativa Japonica) 104 Bulk export of data with BioMart, Demo
BioMart Salmo salar (Atlantic salmon) 109 Exporting gene data with BioMart, demo
BioMart Sheep (Ovis aries) 104 Bulk export of Ensembl data with BioMart, demo
BioMart Sheep (Ovis aries) 104 Finding genes linked to a GO term, Demo
BioMart Human 104 Exporting data for genetic variants with BioMart, Demo
BioMart Triticum aestivum (wheat) 56 Exporting wheat gene data with BioMart, demo
BioMart Zebrafish 107 Exporting gene data with BioMart, demo
Browsing genomic regions Atlantic Salmon 109 Exploring genomic regions in Ensembl, Demo
Browsing genomic regions Escherichia coli str. K-12 substr. MG1655 (GCA_000005845) 56 Exploring genomic regions in Ensembl, Demo
Browsing genomic regions Chicken (Gallus gallus) 111 Exploring genomic regions in Ensembl, Demo
Browsing genomic regions Human 104 Exploring genomic regions in Ensembl, Demo
Browsing genomic regions Mosquito (Anopheles gambiae) 104 Exploring genomic regions in Ensembl, Demo
Browsing genomic regions Triticum aestivum (wheat) 56 Exploring genomic regions in Ensembl Plants, Demo
Browsing genomic regions zebrafish 106 Exploring genomic regions in Ensembl, Demo
Comparative Genomics Salmo salar (Atlantic salmon) 109 Gene trees and homologues, demo
Comparative Genomics Zebrafish 107 Whole genome alignments, demo
Comparative Genomics Zebrafish 107 Gene trees and homologues, demo
Comparative genomics Human 105 Gene trees and homologues, Demo
Comparative genomics Human 105 Whole genome alignments, Demo
Comparative genomics Cattle (Bos taurus) 111 Finding homologues and gene trees, demo
Comparative genomics Fusarium solani (v2.0) 56 Whole-genome alignments, Demo
Comparative genomics Saccharomyces cerevisiae R64-1-1 56 Gene trees and homologues, Demo
Comparative genomics Mosquito (Anopheles gambiae) 104 Gene trees and homologues, Demo
Comparative genomics Pig (Sus scrofa) 111 Aligning genomic regions, demo
Comparative genomics Pig (Sus scrofa) 111 Comparative genomics, demo
Comparative genomics Rice (Oryza sativa Japonica) 104 Whole genome alignments, Demo
Comparative genomics Triticum aestivum (wheat) 57 Gene trees and homologues, Demo
Comparative genomics Salmo salar (Atlantic salmon) 109 Whole-genome alignments, Demo
Comparative genomics Triticum aestivum (wheat) 56 Whole genome alignments, Demo
Cultivar comparative genomics Plants - Oryza sativa Japonica Group 111 Finding comparative genomics data for cultivars in Ensembl Plants, Demo
Custom data Human 104 Custom data, Demo
Custom data Zymoseptoria tritici 104 Uploading small files, Demo
Custom data Arabidopsis thaliana 51 Custom data, Demo
Gene expression and regulation Homo sapiens (human) 111 Features that regulate gene expression, Demo
Genes and transcripts Atlantic Salmon 109 Exploring Atlantic Salmon genes and transcripts, demo
Genes and transcripts Zymoseptoria tritici 104 Finding genes and transcripts in Ensembl, Demo
Genes and transcripts Escherichia coli str. K-12 substr. MG1655 (GCA_000005845) 56 Genes and transcripts in Ensembl Bacteria, Demo
Genes and transcripts Drosophila melanogaster 104 Exploring a Drosophila melanogaster gene, Demo
Genes and transcripts Human 105 Human genes and transcripts in Ensembl, Demo
Genes and transcripts Pig (Sus scrofa) 111 Genes and transcripts in Ensembl, Demo
Genes and transcripts Arabidopsis thaliana 54 Genes and transcripts in Ensembl Plants, Demo
Genes and transcripts Rice (Oryza sativa Japonica) 104 Exploring a gene in Rice, demo
Genes and transcripts Triticum aestivum (wheat) 56 Genes and transcripts in Ensembl Plants, Demo
Genes and transcripts Zebrafish 104 Exploring zebrafish genes and transcripts, demo
Genes and variants Human 110 Finding information about genes and variants in Ensembl, Demo
HPRC data Homo sapiens (Human) 111 Accessing HPRC data in Ensembl Rapid Release, Demo
REST API Human 104 Fetching data using the Ensembl REST API, demo
Rapid Release Panda 105 Accessing newly annotated genomes in Ensembl Rapid Release, Demo
Rapid Release Rapid release- Cucumber beetle 111 Finding species and assembly information on the Ensembl Rapid release genome browser, Demo
Rapid release Panda 104 Accessing newly annotated genomes in Ensembl Rapid Release, Demo
Species and genome assemblies Atlantic Salmon 109 Finding information about chicken, Demo
Species and genome assemblies Chicken 111 Finding information about chicken, Demo
Species and genome assemblies Plants - Arabidopsis thaliana 104 Finding information about species and genomes in Ensembl Plants, Demo
Species and genome assemblies All 109 Finding information about species and genomes in Ensembl, Demo
Species and genome assemblies Triticum aestivum (wheat) 56 Finding information about wheat species and genomes in Ensembl Plants, Demo
Species and genome assemblies zebrafish 106 Finding information about zebrafish, Demo
VEP Atlantic Salmon 109 Annotating genetic variants with the VEP, Demo
VEP Human 109 Annotating genetic variants with the VEP, Demo
VEP Saccharomyces cerevisiae R64-1-1 56 Annotating genetic variants with VEP, demo
VEP Human 104 Annotating genetic variants with the VEP, Demo
VEP Human 110 Annotating genetic variants with the VEP, Demo
VEP Mosquito (Anopheles gambiae) 104 Determining the effect of variants on genes with the VEP, demo
VEP pig (Sus_scrofa) 111 Annotating genetic variants with the VEP, Demo
VEP Triticum aestivum (wheat) 57 Command-line VEP via Docker, Demo
VEP Triticum aestivum (wheat) 57 Annotating genetic variants with the VEP, Demo
VEP Sheep (Ovis aries) 104 Annotating genetic variants with the VEP, Demo
Variation Atlantic Salmon 109 Finding Atlantic salmon genetic variation in Ensembl, demo
Variation Chicken (Gallus gallus) 111 Finding genetic variation data, demo
Variation Saccharomyces cerevisiae R64-1-1 56 Finding genetic variation in Ensembl, demo
Variation Human 105 Exploring variants in Ensembl, Demo
Variation Oryza sativa Japonica (rice) 57 Exploring variants in Ensembl Plants, Demo
Variation Triticum aestivum (wheat) 56 Finding genetic variation in Ensembl, demo
Variation Zebrafish 107 Finding zebrafish genetic variation in Ensembl, demo
“Plants Browser Introduction” “Wheat (Tritium aestivum)” 105 Genes, transcripts and genomic regions in Ensembl Plants, Demo

Questions and Answers

This table contains questions and answers. In Ensembl-run workshops, we ask the participants to work through these by themselves, helping out where needed.

Topic Species Updated Exercise
BioMart Chicken 104 Export sequences in FASTA format
BioMart Triticum aestivum (wheat) 56 Get genes by protein domain
BioMart Human 104 BioMart: genes associated with obesity
BioMart Human, mouse 104 Find genes associated with array probes
BioMart Saccharomyces cerevisiae 56 Ensembl Fungi: variation data in the Saccharomyces cerevisiae mitochondrial genome
BioMart Homo sapiens (human) 109 Convert IDs using BioMart
BioMart Human 104 Exporting regulatory features with BioMart
BioMart Human 104 Exporting histone modification sites with BioMart
BioMart Homo sapiens (human), Ciona savignyi 104 Exporting homologues with BioMart
BioMart Human, dog 104 Exporting homologues with BioMart
BioMart Human 105 Exporting paralogues with BioMart
BioMart Mouse 104 Finding genes by protein domain
BioMart Trichinella spiralis 104 Finding genes by protein domain
BioMart Tetranychus urticae 104 Finding genes by protein domain
BioMart Human, Ciona savignyi 104 Exporting homologues with BioMart
BioMart Human 104 Export structural variants
BioMart Cattle 104 Export structural variants
BioMart Barley (Hordeum vulgare) 110 Export homologues
BioMart Cattle, chicken 104 Exporting homologues with BioMart
BioMart Pig 111 BioMart: Convert IDs
BioMart Wheat (Triticum aestivum) 104 BioMart Convert IDs
BioMart Human, mouse 104 BioMart: variants in renal carcinoma
BioMart Human 104 Finding variants in transcription factor binding motifs with BioMart
BioMart Tomato (Solanum lycopersicum) 104 Retrieve a list of SNPs from the tomato genome
BioMart Zebrafish 104 BioMart Convert IDs
BioMart Cyprinus carpio carpio (common carp), Oncorhynchus mykiss (rainbow trout) 109 Exporting homologues with BioMart
BioMart Chicken (_Gallus gallus_) 111 BioMart: Finding genes by protein domain
BioMart Chicken 111 BioMart: Find genes associated with array probes
BioMart Trypanosoma brucei, Leishmania major 56 Ensembl Protists: exporting homologues with BioMart
BioMart Leishmania major 104 Leishmania: Browser and BioMart
BioMart Arabidopsis thaliana 104 Mapping microarray probes to genes
BioMart Sparus aurata (Gilthead seabream) 109 Convert IDs using BioMart
BioMart Solanum tuberosum (potato), Zea mays (maize) 56 Ensembl Plants: finding genes by protein domain
BioMart Arabidopsis thaliana 56 Mapping Uniprot IDs in Ensembl Plants
BioMart Zebrafish 104 Export structural variants
BioMart Zebrafish, mouse 104 Find genes associated with array probes
Biomart Zebrafish 107 Zebrafish covert ids
Biomart Zebrafish 107 Export homologues
Biomart Zebrafish 107 Exporting paralogues with BioMart
Biomart Zebrafish 107 Zebrafish Export structural variants
Biomart Zebrafish 107 Finding genes by protein domain
Browsing genomic regions Arabidopsis thaliana 104 Arabidopsis MIR395 region
Browsing genomic regions Plasmodium vivax 104 Ensembl Protists: the Plasmodium vivax genome
Browsing genomic regions Chicken 111 Exploring a genomic region in chicken
Browsing genomic regions Cattle 104 Exploring a genomic region in cow
Browsing genomic regions Coprinopsis cinerea okayama 56 Exploring a region in Coprinopsis cinerea okayama
Browsing genomic regions Gilthead seabream 109 Exploring a genomic region in Gilthead seabream
Browsing genomic regions Grape (Vitis vinifera) 104 Grape MADS4 region
Browsing genomic regions Honeybee (Apis mellifera) 104 Exploring a genomic region in they honeybee
Browsing genomic regions Human 109 Exploring assembly exceptions in human
Browsing genomic regions Human 109 Exploring a genomic region in human
Browsing genomic regions Human 109 Exploring CRISPR sites in a human genomic region
Browsing genomic regions Mosquito (Anopheles gambiae) 104 Exploring a genomic region in Anopheles gambiae
Browsing genomic regions Mouse 109 Exploring a genomic region in mouse
Browsing genomic regions Pig 111 Exploring a genomic region in pig
Browsing genomic regions Rainbow trout 109 Exploring a genomic region in Rainbow trout
Browsing genomic regions Triticum aestivum (wheat) 56 Exploring a wheat region
Browsing genomic regions Oryza sativa Japonica (rice) 56 Exploring a genomic region in Oryza sativa Japonica (rice)
Browsing genomic regions Salmonella enterica 56 Exploring a genomic region in Salmonella enterica
Browsing genomic regions Staphylococcus aureus subsp. aureus NCTC 832 56 Exploring a genomic region in Staphylococcus aureus
Browsing genomic regions Sheep 104 Exploring a genomic region in texel sheep
Browsing genomic regions Turkey 104 Exploring a genomic region in turkey
Browsing genomic regions Zebrafish 107 Exploring repeats
Browsing genomic regions Zebrafish 107 Exploring a genomic region in zebrafish
Comparative genomics Human, chicken, turkey 104 Orthologues, paralogues and gene trees for the human VEGFA gene
Comparative genomics Zebra finch 104 Whole genome alignments
Comparative genomics Barley (Hordeum vulgare), Brachypodium distachyon 104 Whole genome alignments
Comparative genomics Chicken 111 Orthologues and gene trees for the chicken BRAF gene
Comparative genomics Cattle (Bos taurus) 104 Whole genome alignments
Comparative genomics Cattle 109 Cow orthologues
Comparative genomics Zebrafish 104 Whole genome alignments
Comparative genomics Arabidopsis thaliana 104 Arabidopsis alignments
Comparative genomics Arabidopsis thaliana 56 Finding orthologues and gene trees of the Arabidopsis thaliana FUM1 gene
Comparative genomics Human 109 Whole genome alignments
Comparative genomics Human, Chicken 104 Synteny
Comparative genomics Homo sapiens (human) 109 Orthologues and gene trees for the human BRAF gene
Comparative genomics Maize (Zea mays) 104 Orthologues, paralogues and gene trees for the maize Zm00001d015746 gene
Comparative genomics Homo sapiens (mouse), Mus musculus (mouse) 109 Exploring a genomic region between in mouse and human
Comparative genomics Mosquito (Anopheles gambiae) 104 Synteny
Comparative genomics Bacillus subtilis subsp. subtilis str. 168 (GCA_000009045) 56 Pan-taxonomic comparative genomics data in Ensembl Bacteria
Comparative genomics Pig 111 Whole genome alignments
Comparative genomics Schizosaccharomyces pombe 56 Orthologues of the Schizosaccharomyces pombe Mcm6 gene
Comparative genomics Oryza sativa Japonica (rice), Triticum aestivum (wheat) 56 Finding orthologous genes for a root transporter in Oryza sativa Japonica (rice)
Comparative genomics Zebrafish 104 Zebrafish alignments
Comparative genomics Mosquito (Anopheles gambiae) 104 Orthologues of the Anopheles gambiae SCRB9 gene
Comparative genomics Dicentrarchus labrax (European seabass) 109 Exploring European seabass pax6b orthologues
Comparative genomics Sheep, pig 104 Synteny
Comparative genomics Scophthalmus maximus (turbot) 109 Gene tree of the turbot clocka gene
Comparative genomics Triticum aestivum (wheat) 56 Homologues and gene trees for the Triticum aestivum (wheat) RHT1 gene
Comparative genomics Triticum aestivum (wheat) 56 Exploring whole-genome alignments for Triticum aestivum (wheat)
Comparative genomics Zebrafish 107 Zebrafish Synteny
Comparative genomics Zebrafish 107 Zebrafish alignments
Comparative genomics Zebrafish 107 Orthologues and gene trees for the zebrafish braf gene.
Custom data Homo sapiens (human) 109 Attaching the ENCODE track hub in human
Custom data Arabidopsis thaliana 104 Viewing gene features on the Arabidopsis karyotype
Custom data Human 104 Displaying BAM files in Ensembl
Custom data Gluconacetobacter diazotrophicus 104 Adding Wiggle files to Ensembl Bacteria
Custom data Schizosaccharomyces pombe 104 Adding BAM files to Ensembl Fungi
Custom data Zea mays 104 Adding Wiggle files to Ensembl Plants
Custom data Solanum lycopersicum 104 Adding track hubs to Ensembl Plants
Custom data Mouse 104 Viewing gene features on the mouse karyotype
Ensembl species Zebrafish 107 Poecilia
Ensembl species Zebrafish 107 Hagfish
Gene expression and regulation Homo sapiens (human) 111 Regulatory features in human
Gene expression and regulation Homo sapiens (human) 111 Regulatory features between INSIG1 and BLACE in human
Genes and Transcripts Common carp 109 Exploring the Common carp prkci gene
Genes and Transcripts Zebrafish 107 Exploring the zebrafish prkci gene
Genes and transcripts Drosophila melanogaster 104 Exploring the Drosophila ZAP3 gene
Genes and transcripts Clostridium sporogenes (GCA_001444695) 56 Exploring a bacterial gene in Clostridium sporogenes
Genes and transcripts Escherichia coli str. K-12 substr. MG1655 (GCA_000005845) 56 Exploring a gene in Escherichia coli
Genes and transcripts Mosquito (Anopheles gambiae) 104 Mosquito: protein function
Genes and transcripts Turbot 109 Exploring the Turbot pcsk2 gene
Genes and transcripts Triticum aestivum (wheat) 56 Exploring a wheat gene
Genes and transcripts Mouse 104 Mouse zinc finger protein
Genes and transcripts Chlamydomonas reinhardtii 104 Exploring a Chlamydomonas reinhardtii gene
Genes and transcripts Atta cephalotes (leaf-cutter ant) 104 Exploring a leaf-cutter ant gene
Genes and transcripts Arabidopsis thaliana 56 Exploring the CCD7 gene in Arabidopsis thaliana
Genes and transcripts Arabidopsis thaliana 106 Exploring a plant gene (Arabidopsis thaliana)
Genes and transcripts zebrafish 104 Finding RNASeq data for the zebrafish cdk1 gene
Genes and transcripts Chicken 111 Exploring the chicken MYH9 gene
Genes and transcripts Cattle 104 Exploring a cow gene
Genes and transcripts Dog 104 Exploring the dog DTHD1 gene
Genes and transcripts Tomato (Solanum lycopersicum) 104 Exploring a defence-related gene in Tomato, Solanum lycopersicum
Genes and transcripts Grape (Vitis vinifera) 104 Exploring a plant gene (Vitis vinifera, grape)
Genes and transcripts Human 109 Exploring the MYH9 gene in human
Genes and transcripts Human 109 Finding a gene associated with a phenotype
Genes and transcripts Lottia gigantea 104 Exploring a Lottia gigantea gene
Genes and transcripts Magnaporthe oryzae (MG8) 56 Exploring a gene in Magnaporthe oryzae
Genes and transcripts Mouse 104 Exploring the Clu gene in mouse
Genes and transcripts Mus musculus (mouse) 109 Exploring the Dpp6 gene in mouse
Genes and transcripts Mosquito (Anopheles gambiae) 104 Exploring an Anopheles gambiae gene
Genes and transcripts Plasmodium falciparum (Malaria parasite) 56 Exploring a gene in Plasmodium falciparum
Genes and transcripts Tomato (Solanum lycopersicum) 104 Exploring the tomato Solyc03g114600.3 gene
Genes and transcripts Triticum aestivum (wheat) 56 Finding a Triticum aestivum gene
Genes and transcripts Yeast (Saccharomyces cerevisiae) 104 SMC1 in Saccharomyces cerevisiae
Genes and transcripts Zebra finch (Taeniopygia guttata) 104 Exploring a gene in zebra finch
Genes and transcripts Zebrafish 107 Exploring the zebrafish vegfaa gene
Rapid release Wild Bactrian camel, Human 104 Investigate data in Ensembl Rapid Release
Species and genome assemblies Arabidopsis thaliana 104 Arabodopsis
Species and genome assemblies Mycobacterium tuberculosis H37Ra str. ATCC25177 (GCA_000016145) 56 Finding a genome in Ensembl Bacteria
Species and genome assemblies Cattle 104 Cattle previous assemblies
Species and genome assemblies Chicken 111 Chicken assembly
Species and genome assemblies Atlantic cod (Gadus morhua) 104 Cod assembly
Species and genome assemblies Fusarium graminearum 56 Fusarium genus
Species and genome assemblies Anopheles gambiae (mosquito) 111 Mosquito species
Species and genome assemblies Giant panda 111 Panda species
Species and genome assemblies Pig 111 Pig species data
Species and genome assemblies Rice (Oryza sativa Japonica) 56 Oryza sativa Japonic (rice) gene counts
Species and genome assemblies European seabass (Dicentrarchus labrax) 109 Available European seabass assemblies
Species and genome assemblies Sheep 104 Sheep species data
Species and genome assemblies Solanum 56 Solanum genus
Species and genome assemblies Black-legged tick (Ixodes scapularis) 104 Black-legged tick assembly
Species and genome assemblies Turbot 109 Turbot genome assembly
Species and genome assemblies Triticum aestivum (wheat) 56 Triticum aestivum (wheat) cultivars
Species and genome assemblies Threadworm (Strongyloides ratti) 104 Worm assembly
Species and genome assemblies Danio rerio (Zebrafish) 111 Available zebrafish assemblies
Synteny between human and duck Homo sapiens (human), Anas platyrhynchos platyrhynchos (duck) 109 Synteny
VEP Atlantic salmon 109 VEP analysis of variant in Atlantic salmon
VEP Atlantic salmon 109 VEP cdk5r1b Atlantic salmon
VEP Homo sapiens (human) 109 Running CFTR variants through VEP
VEP Homo sapiens (human) 109 VEP analysis of FLG variants in human
VEP Human, mouse 104 VEP with HGVS notation
VEP Chicken (Gallus_gallus) 111 VEP for chicken data
VEP Verticillium dahliae JR2 56 VEP analysis of variants in Verticillium dahliae
VEP Bacteroides fragilis 638R 56 VEP in Ensembl Bacteria
VEP Turkey (Meleagris gallopavo) 104 VEP for turkey data
VEP Triticum aestivum (wheat) 57 Web VEP analysis of variants in Triticum aestivum (wheat)
VEP Homo sapiens (human) 109 VEP analysis of structural variants in human
VEP Zebrafish 104 VEP in zebrafish
VEP Cattle (Bos taurus) 104 VEP using a VCF file
VEP Oryza sativa (rice) 57 Command-line VEP analysis of variants in Oryza sativa (rice) via Docker
VEP Oryza sativa Japonica (rice) 57 Web VEP analysis of variants in Oryza sativa Japonica (rice)
Variation Atlantic salmon 109 Exploring a SNP in Atlantic salmon
Variation Atlantic salmon 109 Exploring sequence variant annotation in Atlantic salmon
Variation Homo sapiens (human) 109 Exploring a SNP in the human genome
Variation Mouse 109 Exploring a SNP in mouse
Variation Human 110 Exploring VNTR in human
Variation Human 104 Exploring sequence variant annotation in human
Variation Human 104 Finding SNPs by rsIDs
Variation Arabidopsis thaliana 57 Exploring a SNP in Arabidopsis
Variation Chicken (Gallus gallus) 108 Exploring a phenotype in chicken
Variation Chicken (Gallus gallus) 111 Exploring a SNP in chicken
Variation Fusarium oxysporum 56 Variation data in Fusarium oxysporum
Variation Mosquito (Anopheles gambiae) 104 Exploring a SNP in Anopheles gambiae
Variation Pig (Sus scrofa) 111 Exploring a variant in pig
Variation Human 104 Structural variants in the CCL3L1 gene
Variation Zebrafish 104 Exploring variants of the zebrafish gene tbx16
Variation Human 109 Human population genetics and phenotype data
Variation Human 108 Exploring sequence variant annotation in human
Variation Human 108 Exploring a SNP in human
Variation Sheep (Ovis aries) 104 Variation data in sheep CD72
Variation Solanum lycopersicum (tomato) 57 Variation data in tomato
Variation Triticum aestivum (wheat) 57 Investigating a variant in wheat
Variation Zebrafish 107 Exploring a SNP in zebrafish
Wrap-up exercise Human, mouse 84 Methylation data in human
Wrap-up exercise Human 104 Wrap-up exercise