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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
Finding species data Multi E103 Species_data
Region in detail view Human E103 Region_in_detail_walkthrough
Region in detail view—SHH Human E103 Region_in_detail_SHH
Region in detail view Plants - wheat E103 wheat_region
Region in chicken livestock - chicken E103 chicken_region_demo
Region in detail metazoa - Anopheles gambiae E103 Region_mozzies
Gene and transcript tabs Human E103 Gene_transcript_tabs_walkthrough
Gene and transcript tabs – OS01G0775500 gene Plants (rice) E103 G&T_riceOS01G0775500
Gene and transcript tabs — SHH Human E103 Genes and transcripts — SHH
Gene and transcript tabs — Mdr65 gene, pesticide resistance Metazoa (Fruitfly) E103 Genes and transcripts — Mdr65
Gene and transcript tabs of a PHI-base annotated gene Fungi - Zymoseptoria tritici E103 ZT_phibase_gene
Gene and transcript tabs plants - barley E103 Barley_gene_demo
Gene and transcript tabs livestock - pig E103 pig_gene_demo
Gene and transcript tabs zebrafish E103 zebrafish_gene_demo
Variation in the browser Human E103 variation_in_the_browser_walkthrough
Variation in the browser – OS01G0775500 gene Plants (rice) E103 variation_riceOS01G0775500
Variation in the browser – SHH Human E103 Variation—SHH
Variation in wheat plants - wheat E103 wheat_variation_demo
Variation in rice plants - rice E103 rice_variation_demo
Variation livestock, bird - chicken E103 chicken_variation_demo
Variation in the browser zebrafish E103 zebrafish_variation_demo
VEP online tool with default format Human E103 VEP_online_tool
VEP in wheat plants - wheat E103 wheat_vep_demo
VEP with coordinates livestock - sheep E103 sheep_vep_demo
VEP coordinates metazoa - Anopheles gambiae E103 mozzie_VEP_demo
Comparative Genomics in the browser Human E103 compara_walkthrough
Whole genome alignments plants - rice E103 rice_alignments_demo
Gene trees and homologues plants - wheat E103 wheat_gene_trees_homologues
Compara gene trees and homologues livestock - cow E103 cow_genetrees_orthologues_demo
Compara alignments livestock - pig E103 pig_alignment_hoxD_demo
Gene trees and homologues metazoa - Anopheles gambiae E103 mozzie_genetrees_homologues_demo
Regulation Human E103 regulation_walkthrough
BioMart walkthrough - human genes Human E103 Demo BioMart
BioMart with variation slant Human E103 variation_biomart
BioMart, variation: barley Plants (barley) E103 BioMart_variationBarley
BioMart, livestock milk orthology Livestock (sheep/ungulates) E103 BioMart GO milk secretion
BioMart query with a wheat region Plants - wheat E103 wheat_biomart_demo
BioMart rice region plants - rice E103 rice_biomart_demo
BioMart gene list metazoa - Anopheles gambiae E103 mozzie_biomart_demo
BioMart sheep gene list livestock - sheep E103 sheep_biomart_demo
Upload BED file to view in Ensembl Human E103 BED_upload
Attach BAM file to view in Ensembl Human E103 BAM_upload
Uploading BED files Fungi - Zymoseptoria tritici E103 fungi_bed
Perform a REST API query Human E103 REST_query

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 E103 Panda
Species information Zebrafish E103 Zebrafish
Species information Pig E103 Pig
Species information Sheep E103 Sheep
Species information Cow E103 cow_info
Species information Chicken E103 chicken_info
Species information Fish (cod) E103 cod_info
Species information Plants (Arabodopsis thaliana) E103 Arabidopsis_info
Species information Wheat (Triticum aestivum) E103 Wheat
Species information Plants (rice) E103 rice_info
Species information Plants (Solanum) E103 Solanum_species_info
Species information metazoa - Ixodes scapularis E103 tick_info
Species information Metazoa (Mosquitoes) E103 Mosquitos
Species information Worm (Strongyloides ratti) E103 Strongyloides ratti
Species information Bacteria (Mycobacterium) E103 Mycobacterium
Species information Fusarium graminearum E103 fusarium_info
Region in Detail Human E103 BRCA2_repeats
Region in Detail - haplotypes Human E103 Haplotypes_patches
Region in Detail Mouse E103 CLU region
Region in Detail Mouse E103 BRCA2_region
Region in Detail Cow E103 Cow_region
Region in Detail Sheep E103 Sheep_region
Region in Detail Turkey E103 LocationTab_Avian
Region in Detail Zebrafish E103 zebrafish_region
Region in Detail Metazoa (Anopheles gambiae) E103 mosquito_region
Region in Detail Metazoa (Honeybee) E103 honeybee_region
Region in Detail Plants (Arabidopsis) E103 MIR395_region
Region in Detail Plants (Grape) E103 MADS4_region
Region in Detail with polyploid view Plants (wheat) E103 region_wheat
Region in Detail Plants (rice) E103 rice_region
Region in Detail Protists (Plasmodium vivax) E103 assembly_vivax
Region in Detail Bacteria (Salmonella enterica) E103 Salmonella_region
Gene Human E103 MYH9_gene
Gene - finding a gene by phenotype Human E103 PAH_gene
Gene + Region Mouse E103 Zfp746_gene
Gene Mouse E103 Mouse_Dpp6_gene
Gene Chicken E103 chicken_myh9
Gene Cow E103 cow_NIPBL
Gene Dog E103 Exploring_the_Dog_DTHD1_gene
Gene Zebrafish E103 zebrafish_vegfaa
Gene expression Zebrafish E103 cdk1_rnaseq
Gene Zebrafinch E103 GeneTab_Avian
Gene Plants (Arabidopsis) E103 Exploring_Arabidopsis_gene
Gene Plants (Wheat) E103 wheat_PSBO
Gene Plants (Grape) E103 Grape_gene
Gene Plants (Tomato) E103 tomato_gene
Gene Plants (Tomato) E103 Tomato defence related gene NCED2
Gene Plants (Wheat) E103 wheat_uba2
Gene Plants (Green algae) E103 Exploring_C_reinhardtii_gene
Gene Metazoa (Anopheles gambiae) E103 Mosquito_genome_proteindomains_GO
Gene Metazoa (Anopheles gambiae) E103 mozzie_para
Gene Metazoa (Drosophila) E103 Drosophila_ZAP3
Gene Metazoa (Leaf cutter ant) E103 Exploring_leaf_cutter_ant_gene
Gene Metazoa (Lottia gigantea) E103 Exploring_lottia_gigantea_gene
Gene + Region Fungi (S. cerevisiae) E103 fungus_gene
Gene Protists (P. falciparum) E103 Exploring_P_falciparum_gene
Gene Bacteria (C. sporogenes) E103 Exploring_bacterial_gene
Gene Bacteria (E. coli) E103 Gene_tab_era
BioMart - convert IDs Human E103 BioMart_RefSeq
BioMart - find orthologues Human/Ciona intestinalis E103 BioMart_orthologues
BioMart - find variants Human E103 BioMart_SVs
BioMart - convert probes to genes Human E103 BioMart_probes
BioMart - Variation Human E103 BioMart_variation
BioMart - Gene - obesity Human E103 BioMart_Genes_obesity
BioMart - Compara Human E103 compara_paralogues
BioMart - Variation Human E103 BioMart_Variation_rsIDs
BioMart - filter by protein domain Mouse E103 BioMart_domains
BioMart - homologues Dog E103 Export_homologues_dog
BioMart - Gene - Domains & Homologues Zebrafish and Human E103 BioMart_Gene_domains_homologues
Biomart - array probes Chicken E103 chicken_probes_biomart
BioMart - FASTA sequence Chicken E103 BioMart_Avian_export_fasta
Biomart - filter by region and domain Chicken E103 chicken_domains_biomart
Biomart - orthologues Cow + Chicken E103 biomart_cow_orthologues
Biomart - convert IDs Pig E103 biomart_pig_refseq
Biomart - variation Cow E103 Export_Structural_Variants_Cow
BioMart - homologues Fish (Stickleback and Human) E103 stickleback_orthologues
BioMart - RefSeq IDs Zebrafish E103 zebrafish_refseq
BioMart - SVs Zebrafish E103 zebrafish_SVs_biomart
BioMart - array probes Zebrafish E103 zebrafish_probes_biomart
BioMart - orthologues Plants (Wheat and Barley) E103 biomart_homologues_plants
BioMart - domains Plants (Potato and maize) E103 biomart_plant_domains
BioMart - ID conversion Plants (Arabidopsis) E103 Uniprot_BioMar
BioMart - probes Plants (Arabidopsis) E103 probes_BioMart
BioMart - ID conversion Plants (Wheat) E103 biomart_plant_refseq
BioMart - Variation Plant (tomato) E103 tomato_variants_biomart
BioMart - Variation Plant (tomato) E103 BioMart_missense_chr6
BioMart - FASTA NCBI Gene ID only Plants (Bread wheat) E103 BioMart_FASTA_NCBI
BioMart + Browser Protists (Leishmania) E103 leishmania_biomart_browser
BioMart - homologues Protsis (Leishmania and Trypanosoma) E103 Export_homologues_Protists
BioMart - filter by protein domains Metazoa (Trichinella spiralis) E103 Finding_genes_by_protein_domain_Trichinella
BioMart genes by domain Metazoa (Tetranychus urticae) E103 mite_domains_biomart
BioMart - Variation Fungi (S. cerevisiae) E103 cerevisiae_variants_mtDNA
Variation Human E103 TAGAP_variant
Variation Human E103 MTHFR_variant
Variation Human E103 structural_variants
Variation Human E103 Variation_NPC1_human
Variation SNPs population genetics Human E103 Variation_rsIDs_human
Variation - STR Human E103 human_STR
Variation Mouse E103 mouse_variant
Variation Pig E103 pig_variant
Variation Chicken E103 chicken_snp
Variation + Phenotype - Rose comb Chicken E103 chicken_rosecomb
Variation Sheep E103 Variation_data_in_sheep_cd72
Variation Sheep and mouse E103 Intro_sheep.docx
Variation Zebrafish E103 zebrafish_snp
Variation Zebrafish E103 tbx16_variants
Variation Plant (Arabidopsis) E103 Variation_tab_ATCDSP32
Variation Plant (Tomato) E103 tomato_variants_location
Variation Metazoa (Anopheles gambiae) E103 mozzie_snp
Variation Fungi (F. oxysporum) E103 Fusarium_variation
VEP Human E103 CFTR_VEP
VEP - HGVS notation Human E103 HGVS_VEP
VEP Turkey E103 VEP_turkey_data
VEP query with a VCF file Cow E103 cow_vcf_vep
VEP coordinates zebrafish E103 atp5o_vep
VEP with a VCF file Plants (Rice) E103 rice_vep_vcf
VEP - indel Bacteria (Bacteroides fragilis) E103 VEP_indel_bacteria
Compara - orthologues Human E103 BRAF_compara
Compara - synteny Human E103 RHO_compara
Compara - Gene tree and homologues Human E103 Gene_tree_VEGFA
Compara - Gene tree,homologues, region comparison Plants(Rice Japonica) E103 Rice arsenic aquaporin channel compara
Compara - pairwise alignments Human E103 BRCA2_compara
Compara - Synteny Human and Chicken E103 Synteny - Avian
Compara - Alignment Human, chimp, birds E103 Genomic_Alignment_BRCA2_human_avian
Compara - orthologues Chicken E103 chicken_braf
Compara - orthologues Cow E103 cow_sardh
Compara - alignments Cow E103 brca2_cow
Compara - synteny Sheep and pig E103 rho_sheep
Compara - Genomic alignment Zebrafinch E103 Genomic_alignments_DBH
Compara - whole genome aligments Zebrafish E103 fish_brca_alignments
Compara - multiple alignments Zebrafish E103 sardh_compara
Compara - whole genome alignments Plants (Barley) E103 barley_alignments
Compara - Whole genome alignment + synteny Plant (Arabidopsis) E103 whole_genome_alignments
Compara - Gene trees Plant (Arabidopsis) E103 gene_tree_1
Compara - Gene trees and homologues Plants (Maize) E103 maize_genetrees
Compara - orthologues Metazoa (Anopheles gambiae) E103 scrb9_orthologues
Compara - synteny Metazoa (Anopheles) E103 mozzie_synteny
Compara - Pan compara Fungi (S. pombe) E103 pombe_orthologues
Regulation Human E103 INSIG_BLACE_regulation_exercise
Regulation Human E103 CTCF_regulation
Advanced: multisection Human E84 PDHA2_advanced
Advanced: VEP, variation mart, REST API Human E103 Wrap-up exercise
Upload gene features on the mouse karyotype Mouse E103 upload_mouse_karyotype