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
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 | Bemisia tabaci (Silverleaf whitefly, Uganda-1) | 59 | Finding protein coding genes with AlphaFold DB import data in Bemisia tabaci |
| 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 | Coffea canephora (coffee), Arabidopsis thaliana | 112 | Exporting homologues with BioMart |
| BioMart | Coffea canephora (coffee) | 112 | Finding genes by protein domain |
| 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 | Homo sapiens (Human) | 11/2024 | Visualising a genomic region in human |
| Browsing genomic regions | Gallus gallus(Chicken) | 112 | Exploring a genomic region in Gallus gallus (Chicken) |
| Browsing genomic regions | Coffea canephora (coffee) | 59 | Exploring a genomic region in coffee |
| Browsing genomic regions | Bos taurus (Cow) | 112 | Exploring a genomic region in Bos taurus (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) | 112 | Exploring a genomic region in Anopheles gambiae |
| Browsing genomic regions | Mouse | 109 | Exploring a genomic region in mouse |
| Browsing genomic regions | Sus scrofa (Pig) | 112 | Exploring a genomic region in Sus scrofa (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) | 59 | 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 | Ovis aries Texel (Sheep) | 112 | Exploring a genomic region in Ovis aries 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 | Gallus gallus (Chicken) | 112 | Orthologues and gene trees for the Gallus gallus (Chicken) BRAF gene |
| Comparative genomics | Coffea canephora (coffee), Arabidopsis thaliana | 59 | Finding orthologous genes for disease resistance gene in Coffea canephora (coffee) |
| 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 | Mosquito (Anopheles gambiae) | 112 | Synteny |
| Comparative genomics | Homo sapiens (mouse), Mus musculus (mouse) | 109 | Exploring a genomic region between in mouse and human |
| Comparative genomics | Bacillus subtilis subsp. subtilis str. 168 (GCA_000009045) | 56 | Pan-taxonomic comparative genomics data in Ensembl Bacteria |
| Comparative genomics | Sus scrofa (Pig) | 112 | Gene trees and homologues in Sus scrofa (Pig) breeds |
| Comparative genomics | Sus scrofa (Pig) | 112 | Whole-genome alignments in Sus scrofa (Pig) |
| Comparative genomics | Schizosaccharomyces pombe | 56 | Orthologues of the Schizosaccharomyces pombe Mcm6 gene |
| Comparative genomics | Oryza sativa Japonica (rice), Triticum aestivum (wheat) | 59 | 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 | Magnaporthe oryzae (MG8) | 59 | Exploring a gene in Magnaporthe oryzae |
| 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) | 59 | Exploring a Triticum aestivum (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 | 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 | Escherichia coli K-12 (ASM584v2) | Exploring the Escherichia coli K-12 genome | |
| Genes and transcripts | Homo sapiens (Human) | Exploring the MYH9 gene in Human | |
| Genes and transcripts | Triticum aestivum (Bread wheat) | Exploring genes in Bread wheat and its cultivars | |
| Genes and transcripts | zebrafish | 104 | Finding RNASeq data for the zebrafish cdk1 gene |
| Genes and transcripts | Gallus gallus (Chicken) | 112 | Exploring the MYH9 gene in Gallus gallus (Chicken) |
| Genes and transcripts | Coffea canephora (Robusta coffee) | 109 | Exploring the FUS3 gene in Coffea canephora (Robusta coffee) |
| Genes and transcripts | Cattle | 104 | Exploring a cow gene |
| Genes and transcripts | Dog | 104 | Exploring the dog DTHD1 gene |
| Genes and transcripts | Rosellinia necatrix (GCA_001444695) | 59 | Exploring a fungal gene in Rosellinia necatrix |
| 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 | Mosquito (Anopheles gambiae) | 112 | Exploring an Anopheles gambiae gene |
| Genes and transcripts | Atta cephalotes (leaf-cutter ant) | 112 | Exploring a leaf-cutter ant gene |
| 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 | Sus scrofa (Pig) | 112 | Exploring the Sus scrofa (Pig) TRAF3 gene |
| Genes and transcripts | Tomato (Solanum lycopersicum) | 112 | Exploring a defence-related gene in Tomato, Solanum lycopersicum |
| Genes and transcripts | Plasmodium falciparum (Malaria parasite) | 59 | 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 | 112 | Finding information about Arabidopsis thaliana |
| 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 | Gallus gallus (Chicken) | 112 | Gallus gallus (Chicken) breeds |
| Species and genome assemblies | Chicken | 111 | Chicken assembly |
| Species and genome assemblies | Atlantic cod (Gadus morhua) | 104 | Cod assembly |
| Species and genome assemblies | Coffea canephora | 112 | Exploring the Coffee genome assembly |
| Species and genome assemblies | Botrytis cinerea | 112 | Exploring the Botrytis cinerea genome |
| Species and genome assemblies | Fusarium graminearum | 56 | Fusarium genus |
| Species and genome assemblies | Anopheles gambiae (mosquito) | 112 | Mosquito species |
| Species and genome assemblies | Giant panda | 111 | Panda species |
| Species and genome assemblies | Pig | 112 | Pig species data |
| Species and genome assemblies | Oryza sativa (Rice) | 59 | Oryza sativa (Rice) cultivars |
| 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 | 59 | 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 | Coffea canephora (coffee) | 59 | Web VEP analysis of variants in Coffea canephora (coffee) |
| VEP | Cattle (Bos taurus) | 104 | VEP using a VCF file |
| VEP | Anopheles gambiae | 112 | Running Anopheles gambiae variants through VEP |
| VEP | Oryza sativa (rice) | 57 | Command-line VEP analysis of variants in Oryza sativa (rice) via Docker |
| VEP | Oryza sativa Japonica (rice) | 59 | Web VEP analysis of variants in Oryza sativa Japonica (rice) |
| VEP | Homo sapiens (human) | 112 | Command-line VEP analysis of variants from a 1000 Genomes Project dataset |
| 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 | Aedes aegypti | 59 | Exploring a SNP in Aedes aegypti |
| Variation | Arabidopsis thaliana | 59 | 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 | Phaseolus vulgaris (Common bean) | 59 | Variation data in Phaseolus vulgaris |
| 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 |
