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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
BioMart Barley (Hordeum vulgare) 104 Data export with BioMart
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 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 Wheat (Triticum aestivum) 104 Exporting wheat gene data with BioMart, demo
Browsing genomic regions Chicken (Gallus gallus) 104 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 Wheat (Triticum aestivum) 104 Exploring genomic regions in Ensembl Plants, Demo
Comparative genomics Human 105 Gene trees and homologues, Demo
Comparative genomics Human 105 Whole genome alignments, Demo
Comparative genomics Cattle (Bos taurus) 104 Finding homologues and gene trees, demo
Comparative genomics Mosquito (Anopheles gambiae) 104 Gene trees and homologues, Demo
Comparative genomics Pig (Sus scrofa) 104 Aligning genomic regions, demo
Comparative genomics Rice (Oryza sativa Japonica) 104 Whole genome alignments, Demo
Comparative genomics Wheat (Triticum aestivum) 104 Gene trees and homologues, 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 regulation Human 104 Features that regulate gene expression, Demo
Genes and transcripts Zymoseptoria tritici 104 Finding genes and transcripts in Ensembl, 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) 104 Genes and transcripts in Ensembl, Demo
Genes and transcripts Barley (Hordeum vulgare) 104 Genes and transcripts in Ensembl Plants, Demo
Genes and transcripts Rice (Oryza sativa Japonica) 104 Exploring a gene in Rice, demo
Genes and transcripts Zebrafish 104 Exploring zebrafish genes and transcripts, demo
Genes and variants Human 104 Finding information about genes and variants in Ensembl, Demo
REST API Human 104 Fetching data using the Ensembl REST API, demo
Rapid release Panda 104 Accessing newly annotated genomes in Ensembl Rapid Release, Demo
Species and genome assemblies Plants - Arabidopsis thaliana 104 Finding information about species and genomes in Ensembl Plants, Demo
Species and genome assemblies All 104 Finding information about species and genomes in Ensembl, Demo
VEP Human 104 Annotating genetic variants with the VEP, Demo
VEP Human 104 Annotating genetic variants with the VEP, Demo
VEP Mosquito (Anopheles gambiae) 104 Determining the effect of variants on genes with the VEP, demo
VEP Wheat (triticum aestivum) 104 Annotating genetic variants with the VEP, Demo
VEP Sheep (Ovis aries) 104 Annotating genetic variants with the VEP, Demo
Variation Chicken (Gallus gallus) 104 Finding genetic variation data, demo
Variation Human 105 Exploring variants in Ensembl, Demo
Variation Rice (Oryza sativa Japonica) 104 Exploring variants in Ensembl Plants, Demo
Variation Wheat (Triticum aestivum) 104 Finding genetic variation in Ensembl, demo
Variation Zebrafish 104 Finding zebrafish genetic variation in Ensembl, 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 Wheat (Triticum aestivum) 104 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 104 Ensembl Fungi: variation data in the S. cerevisiae mitochondrial genome
BioMart Human 104 BioMart Convert IDs
BioMart Human 104 Exporting regulatory features with BioMart
BioMart Human 104 Exporting histone modification sites with BioMart
BioMart Human, Ciona savignyi 104 Exporting homologues with BioMart
BioMart Human, dog 104 Exporting homologues with BioMart
BioMart Human 104 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) 104 Export homologues
BioMart Cattle, chicken 104 Exporting homologues with BioMart
BioMart Pig 104 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 Chicken (Gallus gallus) 104 Finding genes by protein domain
BioMart Chicken 104 Find genes associated with array probes
BioMart Trypanosoma brucei, Leishmania major 104 Exporting homologues with BioMart
BioMart Leishmania major 104 Leishmania: Browser and BioMart
BioMart Arabidopsis thaliana 104 Mapping microarray probes to genes
BioMart Potato (Solanum tuberosum), Maize (Zea mays) 104 Finding genes by protein domain
BioMart Arabidopsis thaliana 104 Mapping Uniprot IDs
BioMart Zebrafish 104 Export structural variants
BioMart Zebrafish, mouse 104 Find genes associated with array probes
Browsing genomic regions Arabidopsis thaliana 104 Arabidopsis MIR395 region
Browsing genomic regions Plasmodium vivax 104 Ensembl Protists: the Plasmodium vivax genome
Browsing genomic regions Cattle 104 Exploring a genomic region in cow
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 104 Exploring assembly exceptions in human
Browsing genomic regions Human 104 Exploring a genomic region in human
Browsing genomic regions Human 105 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 104 Exploring a genomic region in mouse
Browsing genomic regions Wheat (Triticum aestivum) 104 Exploring a wheat region
Browsing genomic regions Rice (Oryza sativa Japonica) 104 Exploring a genomic region in rice
Browsing genomic regions Salmonella enterica 104 Exploring a genomic region in Salmonella enterica
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 104 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 104 Orthologues and gene trees for the chicken BRAF gene
Comparative genomics Cattle (Bos taurus) 104 Whole genome alignments
Comparative genomics Cattle 105 Cow orthologues
Comparative genomics Zebrafish 104 Whole genome alignments
Comparative genomics Arabidopsis thaliana 104 Arabidopsis alignments
Comparative genomics Arabidopsis thaliana 104 FUM1 orthologues and gene trees
Comparative genomics Human 104 Whole genome alignments
Comparative genomics Human, Chicken 104 Synteny
Comparative genomics Human 105 Orthologues and gene trees for the human BRAF gene
Comparative genomics Human, Dog 104 Synteny
Comparative genomics Maize (Zea mays) 104 Orthologues, paralogues and gene trees for the maize Zm00001d015746 gene
Comparative genomics Human, mouse 104 Exploring a genomic region (mouse and human)
Comparative genomics Mosquito (Anopheles gambiae) 104 Synteny
Comparative genomics Schizosaccharomyces pombe 104 Orthologues for the Schizosaccharomyces pombe mcm6 gene
Comparative genomics Rice (Oryza sativa Japonica), Wheat (Triticum aestivum) 104 Finding orthologous genes for a root transporter in rice
Comparative genomics Zebrafish 104 Zebrafish alignments
Comparative genomics Mosquito (Anopheles gambiae) 104 Orthologues of the Anopheles gambiae SCRB9 gene
Comparative genomics Sheep, pig 104 Synteny
Custom data Human 104 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
Gene expression regulation Human 105 Regulatory features in human
Gene expression regulation Human 104 Gene regulation: Human INSIG1 and BLACE
Genes and transcripts Drosophila melanogaster 104 Exploring the Drosophila ZAP3 gene
Genes and transcripts Bacteria (Clostridium sporogenes) 104 Exploring a bacterial gene (Clostridium sporogenes)
Genes and transcripts Escherichia coli 104 Exploring a gene in E. coli
Genes and transcripts Mosquito (Anopheles gambiae) 104 Mosquito: protein function
Genes and transcripts Wheat 104 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 Leaf-cutter ant (Atta cephalotes) 104 Exploring a leaf-cutter ant gene
Genes and transcripts Arabidopsis thaliana 104 Exploring the Arabidopsis thaliana CCD7 gene
Genes and transcripts zebrafish 104 Finding RNASeq data for the zebrafish cdk1 gene
Genes and transcripts Chicken 104 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 105 Exploring the human MYH9 gene
Genes and transcripts Human 105 Finding a gene associated with a phenotype
Genes and transcripts Lottia gigantea 104 Exploring a Lottia gigantea gene
Genes and transcripts Mouse 104 Exploring the Clu gene in mouse
Genes and transcripts Mouse 105 Exploring the mouse Dpp6 gene
Genes and transcripts Mosquito (Anopheles gambiae) 104 Exploring an Anopheles gambiae gene
Genes and transcripts Malaria parasite (Plasmodium falciparum) 104 Exploring a Plasmodium falciparum gene
Genes and transcripts Tomato (Solanum lycopersicum) 104 Exploring the tomato Solyc03g114600.3 gene
Genes and transcripts Wheat (Triticum aestivum) 104 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 104 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 104 Finding genomes with species search on Ensembl Bacteria
Species and genome assemblies Cattle 104 Cattle previous assemblies
Species and genome assemblies Chicken 104 Chicken assembly
Species and genome assemblies Atlantic cod (Gadus morhua) 104 Cod assembly
Species and genome assemblies Fusarium graminearum 104 Fusarium genus
Species and genome assemblies Mosquito (Anopheles gambiae) 104 Mosquito species
Species and genome assemblies Giant panda 105 Panda species data
Species and genome assemblies Pig 104 Pig species data
Species and genome assemblies Rice (Oryza sativa Japonica) 104 Rice gene counts
Species and genome assemblies Sheep 104 Sheep species data
Species and genome assemblies Solanum 104 Solanum genus
Species and genome assemblies Black-legged tick (Ixodes scapularis) 104 Black-legged tick assembly
Species and genome assemblies Wheat (triticum aestivum) 104 Wheat cultivars
Species and genome assemblies Threadworm (Strongyloides ratti) 104 Worm assembly
Species and genome assemblies Zebrafish (Danio rerio) 104 Available zebrafish assemblies
VEP Human 105 VEP CFTR
VEP Human, mouse 104 VEP with HGVS notation
VEP Bacteroides fragilis 638R 104 VEP in bacteria
VEP Turkey (Meleagris gallopavo) 104 VEP for turkey data
VEP Wheat (Triticum aestivum) 104 VEP analysis of wheat variants
VEP Human 105 Viewing structural variants with the VEP
VEP Zebrafish 104 VEP in zebrafish
VEP Cattle (Bos taurus) 104 VEP using a VCF file
VEP Rice (Oryza sativa Japonica) 104 VEP analysis of rice variants
Variation Human 105 Exploring a SNP in human
Variation Mouse 105 Exploring a SNP in mouse
Variation Human 105 Exploring VNTR in human
Variation Human 104 Exploring sequence variant annotation in human
Variation Human 104 Finding SNPs by rsIDs
Variation Arabidopsis thaliana 104 Exploring a SNP in Arabidopsis
Variation Chicken (Gallus gallus) 104 Exploring a phenotype in chicken
Variation Chicken (Gallus gallus) 104 Exploring a SNP in chicken
Variation Fusarium oxysporum 104 Variation data in fungi
Variation Mosquito (Anopheles gambiae) 104 Exploring a SNP in Anopheles gambiae
Variation Pig (Sus scrofa) 104 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 105 Human population genetics and phenotype data
Variation Sheep (Ovis aries) 104 Variation data in sheep CD72
Variation Tomato (Solanum lycopersicum) 105 Variation data in the tomato (S. lycopersicum) genome
Variation Wheat (triticum aestivum) 104 Investigating a variant in wheat
Variation Zebrafish 104 Exploring a SNP in zebrafish
Wrap-up exercise Human, mouse 84 Methylation data in human
Wrap-up exercise Human 104 Wrap-up exercise