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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
Basic browser walkthrough - ABCD1 gene Human E76 walk_through_browser_e76.docx
Basic browser walkthrough – OS01G0775500 gene Plants (rice) EG35 RiD_riceOS01G0775500.docx
BioMart walkthrough - human genes Human E84 Demo BioMart
Browser walkthrough sir2gene Fungi (yeast) EG22 walkthrough_yeast.docx
Browser walkthrough DREBgene Plants (bread wheat) EG22 walkthrough_wheat.docx
Browser walkthrough AP1gene Plants (Arabidopsis) EG25 walkthrough_arabidopsis.docx
Finding species data Multi E84/EG31 Species_data
Region in detail view Human E84 Region_in_detail_walkthrough
Region in detail view—SHH Human E84 Region_in_detail_SHH
Gene and transcript tabs Human E84 Gene_transcript_tabs_walkthrough
Gene and transcript tabs – OS01G0775500 gene Plants (rice) EG35 G&T_riceOS01G0775500.docx
Gene and transcript tabs — SHH Human E89 Genes and transcripts — SHH
Variation in the browser Human E84 variation_in_the_browser_walkthrough
Variation in the browser – OS01G0775500 gene Plants (rice) EG35 variation_riceOS01G0775500.docx
Variation in the browser – SHH Human E89 Variation—SHH
VEP online tool with default format Human E84 VEP_online_tool
Compara in the browser Human E84 compara_walkthrough
Regulation Human E84 regulation_walkthrough
Upload BED file to view in Ensembl Human E84 BED_upload
Attach BAM file to view in Ensembl Human E84 BAM_upload
Perform a REST API query Human E84 REST_query
Browser, VEP and REST Bacteria EG22 browser_VEP_Rest.docx
General walkthrough with Variation slant Human E75 variation_browser.docx
BioMart with variation slant Human E75 variation_biomart.docx
BioMart, variation: barley Plants (barley) EG35 BioMart_variationBarley.docx
Region in detail view Plants - wheat EG31 wheat_region
Gene and transcript tabs of a PHI-base annotated gene Fungi - Zymoseptoria tritici EG31 ZT_phibase_gene
BioMart query with a wheat region Plants - wheat EG31 wheat_biomart_demo
Variation in wheat plants - wheat EG31 wheat_variation_demo
VEP in wheat plants - wheat EG31 wheat_vep_demo
Whole genome alignments plants - rice EG31 rice_alignments_demo
Gene trees and homologues plants - wheat EG31 wheat_gene_trees_homologues
Uploading BED files Fungi - Zymoseptoria tritici EG31 fungi_bed
Attaching RNASeq files from the Track Hub Registry plants - rice EG31 Rice_RNAseq_trackhub
Gene and transcript tabs plants - barley EG30 Barley_gene_demo
BioMart rice region plants - rice EG30 rice_biomart_demo
Variation in rice plants - rice EG30 rice_variation_demo
Region in cow livestock - cow E83 cow_region_demo
Gene and transcript tabs livestock - pig E83 pig_gene_demo
BioMart sheep gene list livestock - sheep E83 sheep_biomart_demo
Variation livestock, bird - chicken E83 chicken_variation_demo
VEP with coordinates livestock - sheep E83 sheep_vep_demo
Compara gene trees and homologues livestock - cow E83 cow_genetrees_orthologues_demo
Compara alignments livestock - pig E83 pig_alignment_hoxD_demo
Region in detail metazoa - Anopheles gambiae EG29 Region_mozzies
Gene and transcript tabs zebrafish E82 zebrafish_gene_demo
BioMart gene list metazoa - Anopheles gambiae EG29 mozzie_biomart_demo
Variation in the browser zebrafish E82 zebrafish_variation_demo
VEP coordinates metazoa - Anopheles gambiae EG29 mozzie_VEP_demo
Gene trees and homologues metazoa - Anopheles gambiae EG29 mozzie_genetrees_homologues_demo
Whole genome alignments zebrafish E82 zebrafish_alignments_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 Walkthrough
Species information Panda E84 Panda
Species information Zebrafish E84 Zebrafish
Species information Pig E90 Pig
Species information Sheep E90 Sheep
Species information Cow E83 cow_info
Species information Chicken E83 chicken_info
Species information Fish (cod) E84 cod_info
Species information Plants (Arabodopsis thaliana) EG31 Arabidopsis_info
Species information Wheat (Triticum aestivum) EG38 Wheat
Species information Plants (rice) EG31 rice_info
Species information Plants (Solanum) EG30 Solanum_species_info
Species information metazoa - Ixodes scapularis EG29 tick_info
Species information Metazoa (Mosquitoes) EG31 Mosquitos
Species information Worm (Strongyloides ratti) EG37 Strongyloides ratti
Species information Bacteria (Belliella baltica) EG31 Belliela_baltica
Species information on INSDC annotated species Fungi (Fusarium) EG31 fusarium_info
Region in Detail Human E84 BRCA2_clones
Region in Detail - haplotypes Human E84 Haplotypes_patches
Region in Detail Human E68 LocationTab_Lactase.pptx
Region in Detail Mouse E91 CLU region
Region in Detail Mouse E84 BRCA2_region
Region in Detail Mouse E75 Ush1c_region.docx
Region in Detail (RNASeq, sequence variants) Mouse and Human E76 mouse_location_chr4
Region in Detail Cow E90 Cow_region
Region in Detail Sheep E90 Sheep_region
Region in Detail Turkey E75 LocationTab_Avian.docx
Region in Detail Zebrafish E91 zebrafish_region
Region in Detail Metazoa (Anopheles gambiae) EG38 mosquito_region
Region in Detail Metazoa (Honeybee) EG38 honeybee_region
Region in Detail Plants (Arabidopsis) EG22 MIR395_region.docx
Region in Detail Plants (Grape) EG22 MADS4_region.docx
Region in Detail with polyploid view Plants (wheat) EG31 region_wheat_scaffold
Region in Detail Plants (rice) EG38 rice_region
Region in Detail Plants (Bread wheat) EG22 Genomic_location_bread_wheat.docx
Region in Detail Protists (Plasmodium vivax) EG22 assembly_vivax.docx
Region in Detail Bacteria (Salmonella enterica) E38 Salmonella_region
Region in Detail Bacteria (E. coli) EG22 Location_tab_proV.docx
Gene Human E84 MYH9_gene
Gene - finding a gene by phenotype Human E84 PAH_gene
Gene + Region Mouse E75 PVRL2_gene.docx
Gene + Region Mouse E75 Zfp746_gene.docx
Gene Mouse E84 Mouse_Dpp6_gene
Gene Mouse E75 Chd7_gene.docx
Gene Chicken E90 chicken_myh9
Gene Cow E90 cow_NIPBL
Gene Dog E91 Exploring_the_Dog_DTHD1_gene
Gene Pig E90 pig_phenotype
Gene Zebrafish E91 zebrafish_vegfaa
Gene expression Zebrafish E91 cdk1_rnaseq
Gene Zebrafinch E75 GeneTab_Avian.docx
Gene Plants (Arabidopsis) EG38 Exploring_Arabidopsis_gene
Gene Plants (Potato) EG22 ASC-1_gene.docx
Gene Plants (Wheat) EG31 wheat_PSBO
Gene Plants (Grape) EG38 Grape_gene
Gene Plants (Tomato) EG30 tomato_gene
Gene Plants (Wheat) EG31 wheat_uba2
Gene Plants (Green algae) EG38 Exploring_C_reinhardtii_gene
Gene Metazoa (Anopheles gambiae) EG22 Mosquito_genome_proteindomains_GO.docx
Gene Metazoa (Anopheles gambiae) EG29 mozzie_para
Gene Metazoa (Drosophila) EG31 Drosophila_ZAP3
Gene Metazoa (Leaf cutter ant) EG38 Exploring_leaf_cutter_ant_gene
Gene Metazoa (Lottia gigantea) EG38 Exploring_lottia_gigantea_gene
Gene + Region Fungi (S. cerevisiae) EG20 fungus_gene.docx
Gene Protists (P. falciparum) EG38 Exploring_P_falciparum_gene
Gene Bacteria (C. sporogenes) EG38 Exploring_bacterial_gene
Gene Bacteria (E. coli) EG21 Ecoli_operon.docx
Gene Bacteria (E. coli) EG22 Gene_tab_era.docx
BioMart - convert IDs Human E84 BioMart_RefSeq
BioMart - find orthologues Human/Ciona intestinalis E84 BioMart_orthologues
BioMart - find variants Human E84 BioMart_SVs
BioMart - convert probes to genes Human E84 BioMart_probes
BioMart - Variation Human E84 BioMart_variation
BioMart - Regulation Human E84 regulation_biomart
BioMart - Gene - obesity Human E71 BioMart_Genes_obesity.docx
BioMart - Compara Human E84 compara_paralogues
BioMart - Variation Human E71 BioMart_Variation_rsIDs.docx
BioMart - filter by protein domain Mouse E84 BioMart_domains
BioMart - homologues Dog E91 Export_homologues_dog
BioMart - Gene - Domains & Homologues Zebrafish and Human E71 BioMart_Gene_domains_homologs.docx
Biomart - array probes Chicken E83 chicken_probes_biomart
BioMart - Affy Probes Chicken E75 BioMart_Avian_probes.docx
BioMart - FASTA sequence Chicken E75 BioMart_Avian_export_fasta.docx
Biomart - filter by region and domain Chicken E83 chicken_domains_biomart
Biomart - orthologues Cow + Chicken E83 biomart_cow_orthologues
Biomart - convert IDs Pig E83 biomart_pig_refseq
Biomart - variation Cow E90 Export_Structural_Variants_Cow
BioMart - homologues Fish (Stickleback and Human) E82 stickleback_orthologues
BioMart - RefSeq IDs Zebrafish E82 zebrafish_refseq
BioMart - SVs Zebrafish E82 zebrafish_SVs_biomart
BioMart - array probes Zebrafish E82 zebrafish_probes_biomart
BioMart - orthologues Plants (Wheat and Barley) EG31 biomart_homologues_plants
BioMart - domains Plants (Potato and maize) EG31 biomart_plant_domains
BioMart - ID conversion Plants (Arabidopsis) EG22 Uniprot_BioMart.docx
BioMart - probes Plants (Arabidopsis) EG22 probes_BioMart.docx
BioMart - ID conversion Plants (Wheat) EG31 biomart_plant_refseq
BioMart - FASTA sequence Plants (Bread wheat) EG22 BioMart_bread_wheat.docx
BioMart - Variation Plant (tomato) EG30 tomato_variants_biomart
BioMart - FASTA Entrez Gene ID only Plants (Bread wheat) EG31 BioMart_FASTA_Entrez
BioMart + Browser Protists (Leishmania) EG22 leishmania_biomart_browser.docx
BioMart - homologues Prostsis (Leishmania and Trypanosoma) EG38 Export_homologues_Protists
BioMart - filter by protein domains Metazoa (Trichinella spiralis) EG37 Finding_genes_by_protein_domain_Trichinella
BioMart - protein domains, FASTA export Metazoa (Schistosoma mansoni) EG22 Schistosoma_TM_domain.docx
BioMart genes by domain Metazoa (Tetranychus urticae) EG29 mite_domains_biomart
BioMart with PHIBase filters Fungi (Fusarium graminearum) EG31 Biomart_phibase
BioMart - Variation Fungi (S. cerevisiae) EG22 cerevisiae_variants_mtDNA.docx
Variation Human E84 TAGAP_variant
Variation Human E84 MTHFR_variant
Variation Human E75 structural_variants.docx
Variation Human E73 Variation_NPC1_human.docx
Variation + VEP Human (lung cancer) E73 Variation_VEP_lung_cancer.docx
Variation SNPs population genetics Human E75 Variation_rsIDs_human.docx
Variation CNVs FTO gene Human E75 Variation_CNVs.docx
Variation Mouse E84 mouse_variant
Variation Pig E83 pig_variant
Variation + VEP Turkey E75 Variation_VEP_Avian.docx
Variation Chicken E83 chicken_snp
Variation + Phenotype - Rose comb Chicken E83 chicken_rosecomb
Variation Sheep E90 Variation_data_in_sheep_cd72
Variation Sheep and mouse E76 Intro_sheep.docx
Variation Zebrafish E82 zebrafish_snp
Variation Zebrafish E82 tbx16_variants
Variation Plant (Arabidopsis) EG25 BioMart_missense_chr6.docx
Variation Plant (Tomato) EG38 tomato_variants_location
Variation Plant (Bread wheat) EG31 wheat_missense
Variation Metazoa (Anopheles gambiae) EG29 mozzie_snp
Variation Protists (P. falciparum) EG22 Plasmodium_variation.docx
Variation Fungi (F. oxysporum) EG31 Fusarium_variation
VEP Human E84 CFTR_VEP
VEP - HGVS notation Human E76 HGVS_VEP.docx
VEP - SVs Human E76 SV_VEP.docx
VEP - VCF files Human E76 VCF_VEP.docx test_chr21.vcf
VEP Turkey E90 VEP_turkey_data
VEP query with a VCF file Cow E83 cow_vcf_vep
VEP coordinates zebrafish E82 atp5o_vep
VEP with a VCF file Plants (Rice) EG31 rice_vep_vcf
VEP Ensembl default format Plant (bread wheat) EG25 VEP_default_Ensembl_bread_wheat.docx
VEP - VCF Plants (Bread wheat) EG22 VEP_bread_wheat.docx
VEP - indel Bacteria (Bacteroides fragilis) EG22 VEP_indel_bacteria.docx
Compara - orthologues Human E84 BRAF_compara
Compara - synteny Human E84 RHO_compara
Compara - Gene tree and homologues Human E75 Gene_tree_VEGFA.docx
Compara - pairwise alignments Human E84 BRCA2_compara
Compara - Synteny Human and Chicken E75 Synteny - Avian.docx
Compara - Alignment Human, chimp, birds E75 Genomic_Alignment_BRCA2_human_avian.docx
Compara - orthologues Chicken E83 chicken_braf
Compara - orthologues, protein domains Chicken E76 Intro_chicken.docx
Compara - orthologues Cow E83 cow_sardh
Compara - alignments Cow E83 brca2_cow
Compara - synteny Sheep and pig E83 rho_sheep
Compara - Genomic alignment Zebrafinch E75 Genomic_alignments_DBH.docx
Compara - whole genome aligments Zebrafish E82 fish_brca_alignments
Compara - multiple alignments Zebrafish E84 sardh_compara
Compara - whole genome alignments Plants (Barley) EG31 barley_alignments
Compara - Whole genome alignment + synteny Plant (Arabidopsis) EG25 whole_genome_alignments.docx
Compara - Gene trees + pan compara Plant (Arabidopsis) EG25 gene_tree_FUM1.docx
Compara - Homoeologues + polyploid view Plant (Bread wheat&barley) EG25 gene_tree_FUM1.docx
Compara - Gene trees and homologues Plants (Maize) EG30 maize_genetrees
Compara - Orthologues Plant (Arabidopsis) EG25 Intro_ATHDH_orthologs.docx
Compara - Synteny Metazoa (D. melanogaster) EG22 fruitfly_synteny.docx
Compara - orthologues Metazoa (Anopheles gambiae) EG29 scrb9_orthologues
Compara - synteny Metazoa (Anopheles gambiae and Drosophila melanogaster) EG29 fly_mozzie_synteny
Compara - Pan compara Fungi (S. pombe) EG31 pombe_orthologues
Compara - Gene trees, homologues Fungi (S. cerevisiae) EG22 Fungi_homologs.docx
Compara - Pan-compara Bacteria (Staph. aureus), Human EG21/E74 Pan_compara_bacteria.docx
Compara - orthologues and GO terms Bacteria (Staphylococcus aureus) EG22 Orthologous_and_GO.docx
Regulation Human E84 STX7_regulation
Regulation Human E84 HLA_regulation
Advanced: multisection Human E84 PDHA2_advanced
Advanced: VEP, variation mart, REST API Human E89 Wrap-up exercise
Upload BED file Human E75 upload_human_APC.docx
Upload BAM file Human E75 upload_BAM_human.docx
Upload gene features on the mouse karyotype Mouse E75 upload_mouse_karyotype.docx
Upload GTF file Plants (Bread wheat) EG22 GTF_upload_bread_wheat.docx
Upload BigWig Bacteria (E. coli) EG22 Upload_big_wig.docx
REST-API (several endpoints) human REST_API_human.docx
Browser stats, prediction, GO Plants (bread wheat) EG25 Intro_stats_GO_domains.docx
Three browser RNASeq exercises Human RNASeq_exercises.docx
FindingCorynebacterium genomes, Location tab, Gene families Bacteria (Corynebacterium sp) EG22 Corynebacterium_sp.docx
Finding a gene using sequence search Bacteria (Sulolobus sp) EG22 sequence_search.docx
Browsing GRCh38 (bite sized exercises) Human E76 Bite_sized_GRCh38.docx