Training materials.

Transcription

1 Training materials Ensembl training materials are protected by a CC BY license If you wish to re-use these materials, please credit Ensembl for their creation If you use Ensembl for your work, please cite our papers

2 Exploring Genes and Variants with Ensembl Helen Sparrow Ensembl Outreach EMBL-EBI

3 Today Introduction to Genome Browsers Genes and Transcripts Variation or Browsing Genes and Transcripts Variants Assembly Converter

4 Tomorrow: Variant Effect Predictor The VEP determines the effects of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

5 Objectives What is Ensembl? What type of data can you get in Ensembl? How to navigate the Ensembl browser website How to use Ensembl tools Where to go for help and documentation

6 Course materials tinyurl.com/vepcrete Presentation Coursebook (screenshots of demo) Exercises and Answers

7 Introduction Why do we need genome browsers? 1977: 1st genome to be sequenced (5 kb) 2004: Finished human sequence (3 Gb) 2015: Completion of 1000 Genomes project

8 Why do we need Genome Browsers? CGGCCTTTGGGCTCCGCCTTCAGCTCAAGACTTAACTTCCCTCCCAGCTGTCCCAGATGACGCCATCTGAAATTTCTTGGAAACACGATCACTTTAACGGAATATTGCTGTTTTGGGGAAGTGTTTTACAGCTGCTGGGCACGCTGTATTTGCCTTACTTAAGCCCCTGGTAAT TGCTGTATTCCGAAGACATGCTGATGGGAATTACCAGGCGGCGTTGGTCTCTAACTGGAGCCCTCTGTCCCCACTAGCCACGCGTCACTGGTTAGCGTGATTGAAACTAAATCGTATGAAAATCCTCTTCTCTAGTCGCACTAGCCACGTTTCGAGTGCTTAATGTGGCTAGTG GCACCGGTTTGGACAGCACAGCTGTAAAATGTTCCCATCCTCACAGTAAGCTGTTACCGTTCCAGGAGATGGGACTGAATTAGAATTCAAACAAATTTTCCAGCGCTTCTGAGTTTTACCTCAGTCACATAATAAGGAATGCATCCCTGTGTAAGTGCATTTTGGTCTTCTGTT TTGCAGACTTATTTACCAAGCATTGGAGGAATATCGTAGGTAAAAATGCCTATTGGATCCAAAGAGAGGCCAACATTTTTTGAAATTTTTAAGACACGCTGCAACAAAGCAGGTATTGACAAATTTTATATAACTTTATAAATTACACCGAGAAAGTGTTTTCTAAAAAATGCT TGCTAAAAACCCAGTACGTCACAGTGTTGCTTAGAACCATAAACTGTTCCTTATGTGTGTATAAATCCAGTTAACAACATAATCATCGTTTGCAGGTTAACCACATGATAAATATAGAACGTCTAGTGGATAAAGAGGAAACTGGCCCCTTGACTAGCAGTAGGAACAATTACT AACAAATCAGAAGCATTAATGTTACTTTATGGCAGAAGTTGTCCAACTTTTTGGTTTCAGTACTCCTTATACTCTTAAAAATGATCTAGGACCCCCGGAGTGCTTTTGTTTATGTAGCTTACCATATTAGAAATTTAAAACTAAGAATTTAAGGCTGGGCGTGGTGGCTCACGC CTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCGGATCACTTGAGGCCAGAAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCTATCTCTACTAAAAATACAAAAAATGTGCTGCGTGTGGTGGTGCGTGCCTGTAATCCCAGCTACACGGGAGGTGGAGGCAGGAGAA TCGCTTGAACCCTGGAGGCAGAGGTTGCAGTGAGCCAAGATCATGCCACTGCACTCTAGCCTGGGCCACATAGCATGACTCTGTCTCAAAACAAACAAACAAACAAAAAACTAAGAATTTAAAGTTAATTTACTTAAAAATAATGAAAGCTAACCCATTGCATATTATCACAAC ATTCTTAGGAAAAATAACTTTTTGAAAACAAGTGAGTGGAATAGTTTTTACATTTTTGCAGTTCTCTTTAATGTCTGGCTAAATAGAGATAGCTGGATTCACTTATCTGTGTCTAATCTGTTATTTTGGTAGAAGTATGTGAAAAAAAATTAACCTCACGTTGAAAAAAGGAAT ATTTTAATAGTTTTCAGTTACTTTTTGGTATTTTTCCTTGTACTTTGCATAGATTTTTCAAAGATCTAATAGATATACCATAGGTCTTTCCCATGTCGCAACATCATGCAGTGATTATTTGGAAGATAGTGGTGTTCTGAATTATACAAAGTTTCCAAATATTGATAAATTGCA TTAAACTATTTTAAAAATCTCATTCATTAATACCACCATGGATGTCAGAAAAGTCTTTTAAGATTGGGTAGAAATGAGCCACTGGAAATTCTAATTTTCATTTGAAAGTTCACATTTTGTCATTGACAACAAACTGTTTTCCTTGCAGCAACAAGATCACTTCATTGATTTGTG AGAAAATGTCTACCAAATTATTTAAGTTGAAATAACTTTGTCAGCTGTTCTTTCAAGTAAAAATGACTTTTCATTGAAAAAATTGCTTGTTCAGATCACAGCTCAACATGAGTGCTTTTCTAGGCAGTATTGTACTTCAGTATGCAGAAGTGCTTTATGTATGCTTCCTATTTT GTCAGAGATTATTAAAAGAAGTGCTAAAGCATTGAGCTTCGAAATTAATTTTTACTGCTTCATTAGGACATTCTTACATTAAACTGGCATTATTATTACTATTATTTTTAACAAGGACACTCAGTGGTAAGGAATATAATGGCTACTAGTATTAGTTTGGTGCCACTGCCATAA CTCATGCAAATGTGCCAGCAGTTTTACCCAGCATCATCTTTGCACTGTTGATACAAATGTCAACATCATGAAAAAGGGTTGAAAAAAGGAATATTTTAATAGTTTTCAGTTACTTTTGCTGGGCACGCTGTATTTGCCTTACTTAAGCCCCTGGTAATTGCTGTATTCCGAAGA CATGCTGATGGGAATTACCAGGCGGCGTTGGTCTCTAACTGGAGCCCTCTGTCCCCACTAGCCACGCGTCACTGGTTAGCGTGATTGAAACTAAATCGTATGAAAATCCTCTTCTCTAGTCGCACTAGCCACGTTTCGAGTGCTTAATGTGGCTAGTGGCACCGGTTTGGACAG CACAGCTGTAAAATGTTCCCATCCTCACAGTAAGCTGTTACCGTTCCAGGAGATGGGACTGAATTAGAATTCAAACAAATTTTCCAGCGCTTCTGAGTTTTACCTCAGTCACATAATAAGGAATGCATCCCTGTGTAAGTGCATTTTGGTCTTCTGTTTTGCAGACTTATTTAC CAAGCATTGGAGGAATATCGTAGGTAAAAATGCCTATTGGATCCAAAGAGAGGCCAACATTTTTTGAAATTTTTAAGACACGCTGCAACAAAGCAGGTATTGACAAATTTTATATAACTTTATAAATTACACCGAGAAAGTGTTTTCTAAAAAATGCTTGCTAAAAACCCAGTA CGTCACAGTGTTGCTTAGAACCATAAACTGTTCCTTATGTGTGTATAAATCCAGTTAACAACATAATCATCGTTTGCAGGTTAACCACATGATAAATATAGAACGTCTAGTGGATAAAGAGGAAACTGGCCCCTTGACTAGCAGTAGGAACAATTACTAACAAATCAGAAGCAT TAATGTTACTTTATGGCAGAAGTTGTCCAACTTTTTGGTTTCAGTACTCCTTATACTCTTAAAAATGATCTAGGACCCCCGGAGTGCTTTTGTTTATGTAGCTTACCATATTAGAAATTTAAAACTAAGAATTTAAGGCTGGGCGTGGTGGCTCACGCCTGTAATCCCAGCACT TTGGGAGGCCGAGGTGGGCGGATCACTTGAGGCCAGAAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCTATCTCTACTAAAAATACAAAAAATGTGCTGCGTGTGGTGGTGCGTGCCTGTAATCCCAGCTACACGGGAGGTGGAGGCAGGAGAATCGCTTGAACCCTGGA GGCAGAGGTTGCAGTGAGCCAAGATCATGCCACTGCACTCTAGCCTGGGCCACATAGCATGACTCTGTCTCAAAACAAACAAACAAACAAAAAACTAAGAATTTAAAGTTAATTTACTTAAAAATAATGAAAGCTAACCCATTGCATATTATCACAACATTCTTAGGAAAAATA ACTTTTTGAAAACAAGTGAGTGGAATAGTTTTTACATTTTTGCAGTTCTCTTTAATGTCTGGCTAAATAGAGATAGCTGGATTCACTTATCTGTGTCTAATCTGTTATTTTGGTAGAAGTATGTGAAAAAAAATTAACCTCACGTTGAAAAAAGGAATATTTTAATAGTTTTCA GTTACTTTTTGGTATTTTTCCTTGTACTTTGCATAGATTTTTCAAAGATCTAATAGATATACCATAGGTCTTTCCCATGTCGCAACATCATGCAGTGATTATTTGGAAGATAGTGGTGTTCTGAATTATACAAAGTTTCCAAATATTGATAAATTGCAGATAAATTGCATTAAA CTATTTTAAAAATCTCATTCATTAATACCACCATGGATGTCAGAAAAGTCTTTTAAGATTGGGTAGAAATGAGCCACTGGAAATTCTAATTTTCATTTGAAAGTTCACATTTTGTCATTGACAACAAACTGTTTTCCTTGCAGCAACAAGATCACTTCATTGATTTGTGAGAAA ATGTCTACCAAATTATTTAAGTTGAAATAACTTTGTCAGCTGTTCTTTCAAGTAAAAATGACTTTTCATTGAAAAAATTGCTTGTTCAGATCACAGCTCAACATGAGTGCTTTTCTAGGCAGTATTGTACTTCAGTATGCAGAAGTGCTTTATGTATGCTTCCTATTTTGTCAG AGATTATTAAAAGAAGTGCTAAAGCATTGAGCTTCGAAATTAATTTTTACTGCTTCATTAGGACATTCTTACATTAAACTGGCATTATTATTACTATTATTTTTAACAAGGACACTCAGTGGTAAGGAATATAATGGCTACTAGTATTAGTTTGGTGCCACTGCCATAACTCAT GCAAATGTGCCAGCAGTTTTACCCAGCATCATCTTTGCACTGTTGATACAAATGTCAACATCATGAAAAAGGGTTGAAAAAAGGAATATTTTAATAGTTTTCAGTTACTTTTGCTGGGCACGCTGTATTTGCCTTACTTAAGCCCCTGGTAATTGCTGTATTCCGAAGACATGC TGATGGGAATTACCAGGCGGCGTTGGTCTCTAACTGGAGCCCTCTGTCCCCACTAGCCACGCGTCACTGGTTAGCGTGATTGAAACTAAATCGTATGAAAATCCTCTTCTCTAGTCGCACTAGCCACGTTTCGAGTGCTTAATGTGGCTAGTGGCACCGGTTTGGACAGCACAG CTGTAAAATGTTCCCATCCTCACAGTAAGCTGTTACCGTTCCAGGAGATGGGACTGAATTAGAATTCAAACAAATTTTCCAGCGCTTCTGAGTTTTACCTCAGTCACATAATAAGGAATGCATCCCTGTGTAAGTGCATTTTGGTCTTCTGTTTTGCAGACTTATTTACCAAGC ATTGGAGGAATATCGTAGGTAAAAATGCCTATTGGATCCAAAGAGAGGCCAACATTTTTTGAAATTTTTAAGACACGCTGCAACAAAGCAGGTATTGACAAATTTTATATAACTTTATAAATTACACCGAGAAAGTGTTTTCTAAAAAATGCTTGCTAAAAACCCAGTACGTCA CAGTGTTGCTTAGAACCATAAACTGTTCCTTATGTGTGTATAAATCCAGTTAACAACATAATCATCGTTTGCAGGTTAACCACATGATAAATATAGAACGTCTAGTGGATAAAGAGGAAACTGGCCCCTTGACTAGCAGTAGGAACAATTACTAACAAATCAGAAGCATTAATG TTACTTTATGGCAGAAGTTGTCCAACTTTTTGGTTTCAGTACTCCTTATACTCTTAAAAATGATCTGGCTAAATAGAGATAGCTGGATTCACTTATCTGTGTCTAATCTGTTATTTTGGTAGAAGTATGTGAAAAAAAATTAACCTCACGTTGAAAAAAGGAATATTTTAATAG TTTTCAGTTACTTTTTGGTATTTTTCCTTGTACTTTGCATAGATTTTTCAAAGATCTAATAGATATACCATAGGTCTTTCCCATGTCGCAACATCATGCAGTGATTATTTGGAAGATAGTGGTGTTCTGAATTATACAAAGTTTCCAAATATTGATAAATTGCAGATAAATTGC ATTAAACTATTTTAAAAATCTCATTCATTAATACCACCATGGATGTCAGAAAAGTCTTTTAAGATTGGGTAGAAATGAGCCACTGGAAATTCTAATTTTCATTTGAAAGTTCACATTTTGTCATTGACAACAAACTGTTTTCCTTGCAGCAACAAGATCACTTCATTGATTTGT GAGAAAATGTCTACCAAATTATTTAAGTTGAAATAACTTTGTCAGCTGTTCTTTCAAGTAAAAATGACTTTTCATTGAAAAAATTGCTTGTTCAGATCACAGCTCAACATGAGTGCTTTTCTAGGCAGTATTGTACTTCAGTATGCAGAAGTGCTTTATGTATGCTTCCTATTT TGTCAGAGATTATTAAAAGAAGTGCTAAAGCATTGAGCTTCGAAATTAATTTTTACTGCTTCATTAGGACATTCTTACATTAAACTGGCATTATTATTACTATTATTTTTAACAAGGACACTCAGTGGTAAGGAATATAATGGCTACTAGTATTAGTTTGGTGCCACTGCCATA ACTCATGCAAATGTGCCAGCAGTTTTACCCAGCATCATCTTTGCACTGTTGATACAAATGTCAACATCATGAAAAAGGGTTGAAAAAAGGAATATTTTAATAGTTTTCAGTTACTTTTGCTGGGCACGCTGTATTTGCCTTACTTAAGCCCCTGGTAATTGCTGTATTCCGAAG Buried in the genome sequence is information about: Function- such as transcripts and proteins Expression- regulatory elements Variation- SNPs, structural variants

9 Why do we need Genome Browsers? CGGCCTTTGGGCTCCGCCTTCAGCTCAAGACTTAACTTCCCTCCCAGCTGTCCCAGATGACGCCATCTGAAATTTCTTGGAAACACGATCACTTTAACGGAATATTGCTGTTTTGGGGAAGTGTTTTACAGCTGCTGGGCACGCTGTATTTGCCTTACTTAAGCCCCTGGTAAT TGCTGTATTCCGAAGACATGCTGATGGGAATTACCAGGCGGCGTTGGTCTCTAACTGGAGCCCTCTGTCCCCACTAGCCACGCGTCACTGGTTAGCGTGATTGAAACTAAATCGTATGAAAATCCTCTTCTCTAGTCGCACTAGCCACGTTTCGAGTGCTTAATGTGGCTAGTG GCACCGGTTTGGACAGCACAGCTGTAAAATGTTCCCATCCTCACAGTAAGCTGTTACCGTTCCAGGAGATGGGACTGAATTAGAATTCAAACAAATTTTCCAGCGCTTCTGAGTTTTACCTCAGTCACATAATAAGGAATGCATCCCTGTGTAAGTGCATTTTGGTCTTCTGTT TTGCAGACTTATTTACCAAGCATTGGAGGAATATCGTAGGTAAAAATGCCTATTGGATCCAAAGAGAGGCCAACATTTTTTGAAATTTTTAAGACACGCTGCAACAAAGCAGGTATTGACAAATTTTATATAACTTTATAAATTACACCGAGAAAGTGTTTTCTAAAAAATGCT TGCTAAAAACCCAGTACGTCACAGTGTTGCTTAGAACCATAAACTGTTCCTTATGTGTGTATAAATCCAGTTAACAACATAATCATCGTTTGCAGGTTAACCACATGATAAATATAGAACGTCTAGTGGATAAAGAGGAAACTGGCCCCTTGACTAGCAGTAGGAACAATTACT AACAAATCAGAAGCATTAATGTTACTTTATGGCAGAAGTTGTCCAACTTTTTGGTTTCAGTACTCCTTATACTCTTAAAAATGATCTAGGACCCCCGGAGTGCTTTTGTTTATGTAGCTTACCATATTAGAAATTTAAAACTAAGAATTTAAGGCTGGGCGTGGTGGCTCACGC CTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCGGATCACTTGAGGCCAGAAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCTATCTCTACTAAAAATACAAAAAATGTGCTGCGTGTGGTGGTGCGTGCCTGTAATCCCAGCTACACGGGAGGTGGAGGCAGGAGAA TCGCTTGAACCCTGGAGGCAGAGGTTGCAGTGAGCCAAGATCATGCCACTGCACTCTAGCCTGGGCCACATAGCATGACTCTGTCTCAAAACAAACAAACAAACAAAAAACTAAGAATTTAAAGTTAATTTACTTAAAAATAATGAAAGCTAACCCATTGCATATTATCACAAC ATTCTTAGGAAAAATAACTTTTTGAAAACAAGTGAGTGGAATAGTTTTTACATTTTTGCAGTTCTCTTTAATGTCTGGCTAAATAGAGATAGCTGGATTCACTTATCTGTGTCTAATCTGTTATTTTGGTAGAAGTATGTGAAAAAAAATTAACCTCACGTTGAAAAAAGGAAT ATTTTAATAGTTTTCAGTTACTTTTTGGTATTTTTCCTTGTACTTTGCATAGATTTTTCAAAGATCTAATAGATATACCATAGGTCTTTCCCATGTCGCAACATCATGCAGTGATTATTTGGAAGATAGTGGTGTTCTGAATTATACAAAGTTTCCAAATATTGATAAATTGCA TTAAACTATTTTAAAAATCTCATTCATTAATACCACCATGGATGTCAGAAAAGTCTTTTAAGATTGGGTAGAAATGAGCCACTGGAAATTCTAATTTTCATTTGAAAGTTCACATTTTGTCATTGACAACAAACTGTTTTCCTTGCAGCAACAAGATCACTTCATTGATTTGTG AGAAAATGTCTACCAAATTATTTAAGTTGAAATAACTTTGTCAGCTGTTCTTTCAAGTAAAAATGACTTTTCATTGAAAAAATTGCTTGTTCAGATCACAGCTCAACATGAGTGCTTTTCTAGGCAGTATTGTACTTCAGTATGCAGAAGTGCTTTATGTATGCTTCCTATTTT GTCAGAGATTATTAAAAGAAGTGCTAAAGCATTGAGCTTCGAAATTAATTTTTACTGCTTCATTAGGACATTCTTACATTAAACTGGCATTATTATTACTATTATTTTTAACAAGGACACTCAGTGGTAAGGAATATAATGGCTACTAGTATTAGTTTGGTGCCACTGCCATAA CTCATGCAAATGTGCCAGCAGTTTTACCCAGCATCATCTTTGCACTGTTGATACAAATGTCAACATCATGAAAAAGGGTTGAAAAAAGGAATATTTTAATAGTTTTCAGTTACTTTTGCTGGGCACGCTGTATTTGCCTTACTTAAGCCCCTGGTAATTGCTGTATTCCGAAGA CATGCTGATGGGAATTACCAGGCGGCGTTGGTCTCTAACTGGAGCCCTCTGTCCCCACTAGCCACGCGTCACTGGTTAGCGTGATTGAAACTAAATCGTATGAAAATCCTCTTCTCTAGTCGCACTAGCCACGTTTCGAGTGCTTAATGTGGCTAGTGGCACCGGTTTGGACAG CACAGCTGTAAAATGTTCCCATCCTCACAGTAAGCTGTTACCGTTCCAGGAGATGGGACTGAATTAGAATTCAAACAAATTTTCCAGCGCTTCTGAGTTTTACCTCAGTCACATAATAAGGAATGCATCCCTGTGTAAGTGCATTTTGGTCTTCTGTTTTGCAGACTTATTTAC CAAGCATTGGAGGAATATCGTAGGTAAAAATGCCTATTGGATCCAAAGAGAGGCCAACATTTTTTGAAATTTTTAAGACACGCTGCAACAAAGCAGGTATTGACAAATTTTATATAACTTTATAAATTACACCGAGAAAGTGTTTTCTAAAAAATGCTTGCTAAAAACCCAGTA CGTCACAGTGTTGCTTAGAACCATAAACTGTTCCTTATGTGTGTATAAATCCAGTTAACAACATAATCATCGTTTGCAGGTTAACCACATGATAAATATAGAACGTCTAGTGGATAAAGAGGAAACTGGCCCCTTGACTAGCAGTAGGAACAATTACTAACAAATCAGAAGCAT TAATGTTACTTTATGGCAGAAGTTGTCCAACTTTTTGGTTTCAGTACTCCTTATACTCTTAAAAATGATCTAGGACCCCCGGAGTGCTTTTGTTTATGTAGCTTACCATATTAGAAATTTAAAACTAAGAATTTAAGGCTGGGCGTGGTGGCTCACGCCTGTAATCCCAGCACT TTGGGAGGCCGAGGTGGGCGGATCACTTGAGGCCAGAAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCTATCTCTACTAAAAATACAAAAAATGTGCTGCGTGTGGTGGTGCGTGCCTGTAATCCCAGCTACACGGGAGGTGGAGGCAGGAGAATCGCTTGAACCCTGGA GGCAGAGGTTGCAGTGAGCCAAGATCATGCCACTGCACTCTAGCCTGGGCCACATAGCATGACTCTGTCTCAAAACAAACAAACAAACAAAAAACTAAGAATTTAAAGTTAATTTACTTAAAAATAATGAAAGCTAACCCATTGCATATTATCACAACATTCTTAGGAAAAATA ACTTTTTGAAAACAAGTGAGTGGAATAGTTTTTACATTTTTGCAGTTCTCTTTAATGTCTGGCTAAATAGAGATAGCTGGATTCACTTATCTGTGTCTAATCTGTTATTTTGGTAGAAGTATGTGAAAAAAAATTAACCTCACGTTGAAAAAAGGAATATTTTAATAGTTTTCA GTTACTTTTTGGTATTTTTCCTTGTACTTTGCATAGATTTTTCAAAGATCTAATAGATATACCATAGGTCTTTCCCATGTCGCAACATCATGCAGTGATTATTTGGAAGATAGTGGTGTTCTGAATTATACAAAGTTTCCAAATATTGATAAATTGCAGATAAATTGCATTAAA CTATTTTAAAAATCTCATTCATTAATACCACCATGGATGTCAGAAAAGTCTTTTAAGATTGGGTAGAAATGAGCCACTGGAAATTCTAATTTTCATTTGAAAGTTCACATTTTGTCATTGACAACAAACTGTTTTCCTTGCAGCAACAAGATCACTTCATTGATTTGTGAGAAA ATGTCTACCAAATTATTTAAGTTGAAATAACTTTGTCAGCTGTTCTTTCAAGTAAAAATGACTTTTCATTGAAAAAATTGCTTGTTCAGATCACAGCTCAACATGAGTGCTTTTCTAGGCAGTATTGTACTTCAGTATGCAGAAGTGCTTTATGTATGCTTCCTATTTTGTCAG AGATTATTAAAAGAAGTGCTAAAGCATTGAGCTTCGAAATTAATTTTTACTGCTTCATTAGGACATTCTTACATTAAACTGGCATTATTATTACTATTATTTTTAACAAGGACACTCAGTGGTAAGGAATATAATGGCTACTAGTATTAGTTTGGTGCCACTGCCATAACTCAT GCAAATGTGCCAGCAGTTTTACCCAGCATCATCTTTGCACTGTTGATACAAATGTCAACATCATGAAAAAGGGTTGAAAAAAGGAATATTTTAATAGTTTTCAGTTACTTTTGCTGGGCACGCTGTATTTGCCTTACTTAAGCCCCTGGTAATTGCTGTATTCCGAAGACATGC TGATGGGAATTACCAGGCGGCGTTGGTCTCTAACTGGAGCCCTCTGTCCCCACTAGCCACGCGTCACTGGTTAGCGTGATTGAAACTAAATCGTATGAAAATCCTCTTCTCTAGTCGCACTAGCCACGTTTCGAGTGCTTAATGTGGCTAGTGGCACCGGTTTGGACAGCACAG CTGTAAAATGTTCCCATCCTCACAGTAAGCTGTTACCGTTCCAGGAGATGGGACTGAATTAGAATTCAAACAAATTTTCCAGCGCTTCTGAGTTTTACCTCAGTCACATAATAAGGAATGCATCCCTGTGTAAGTGCATTTTGGTCTTCTGTTTTGCAGACTTATTTACCAAGC ATTGGAGGAATATCGTAGGTAAAAATGCCTATTGGATCCAAAGAGAGGCCAACATTTTTTGAAATTTTTAAGACACGCTGCAACAAAGCAGGTATTGACAAATTTTATATAACTTTATAAATTACACCGAGAAAGTGTTTTCTAAAAAATGCTTGCTAAAAACCCAGTACGTCA CAGTGTTGCTTAGAACCATAAACTGTTCCTTATGTGTGTATAAATCCAGTTAACAACATAATCATCGTTTGCAGGTTAACCACATGATAAATATAGAACGTCTAGTGGATAAAGAGGAAACTGGCCCCTTGACTAGCAGTAGGAACAATTACTAACAAATCAGAAGCATTAATG TTACTTTATGGCAGAAGTTGTCCAACTTTTTGGTTTCAGTACTCCTTATACTCTTAAAAATGATCTGGCTAAATAGAGATAGCTGGATTCACTTATCTGTGTCTAATCTGTTATTTTGGTAGAAGTATGTGAAAAAAAATTAACCTCACGTTGAAAAAAGGAATATTTTAATAG TTTTCAGTTACTTTTTGGTATTTTTCCTTGTACTTTGCATAGATTTTTCAAAGATCTAATAGATATACCATAGGTCTTTCCCATGTCGCAACATCATGCAGTGATTATTTGGAAGATAGTGGTGTTCTGAATTATACAAAGTTTCCAAATATTGATAAATTGCAGATAAATTGC ATTAAACTATTTTAAAAATCTCATTCATTAATACCACCATGGATGTCAGAAAAGTCTTTTAAGATTGGGTAGAAATGAGCCACTGGAAATTCTAATTTTCATTTGAAAGTTCACATTTTGTCATTGACAACAAACTGTTTTCCTTGCAGCAACAAGATCACTTCATTGATTTGT GAGAAAATGTCTACCAAATTATTTAAGTTGAAATAACTTTGTCAGCTGTTCTTTCAAGTAAAAATGACTTTTCATTGAAAAAATTGCTTGTTCAGATCACAGCTCAACATGAGTGCTTTTCTAGGCAGTATTGTACTTCAGTATGCAGAAGTGCTTTATGTATGCTTCCTATTT TGTCAGAGATTATTAAAAGAAGTGCTAAAGCATTGAGCTTCGAAATTAATTTTTACTGCTTCATTAGGACATTCTTACATTAAACTGGCATTATTATTACTATTATTTTTAACAAGGACACTCAGTGGTAAGGAATATAATGGCTACTAGTATTAGTTTGGTGCCACTGCCATA ACTCATGCAAATGTGCCAGCAGTTTTACCCAGCATCATCTTTGCACTGTTGATACAAATGTCAACATCATGAAAAAGGGTTGAAAAAAGGAATATTTTAATAGTTTTCAGTTACTTTTGCTGGGCACGCTGTATTTGCCTTACTTAAGCCCCTGGTAATTGCTGTATTCCGAAG nih.gov/mapview

10 Ensembl - more than a browser Import Genome Assemblies Annotate genomes - Genes and transcripts - Variants - Regulatory features - Comparative Genomics Display and export Tools

11 Ensembl Features Gene builds for ~70 species Gene trees Regulatory build (ENCODE) Variation display and VEP Display of user data BioMart (data export) Programmatic access via the APIs Completely Open Source

12 Reference Genome Assemblies GRCh38 (UCSC equivalent is hg38) Current, supported GRCh gaps (UCSC hg19) Limited data updates NCBI36 150,000 gaps (UCSC hg18) No updates

13 Reference Genome contigs BL102 AL476 BL AL CM553 CM IM768 IM

14 Genes and Transcripts EBI is an Outstation of the European Molecular Biology Laboratory.

15 Ensembl and Havana annotation Automatic annotation Manual annotation

16 Automatic gene annotation Genome-wide determination using the Ensembl automated pipeline Predictions based on experimental (biological) data Predictions based on the genomic sequence (ab initio)

17 Transcript annotation

18 Other species Infer genes from homology to other species Eg predict genes in from to the RNAseq data by mapping cdnas/proteins genome

19 Manual gene annotation Gene determination on a case-by-case basis by a person Genome-wide Genes list vega.sanger.ac.uk

20 GENCODE The GENCODE gene set is made up of: Ensembl automatically annotated genes Havana manually annotated genes The merged gene set default gene set for ENCODE 1000 genomes and lots of other major projects

21 Merged Golden transcripts Identical annotation Higher confidence and quality CCDS transcripts Consensus coding DNA sequence set Agreement between EBI, WTSI, UCSC and NCBI

22 Transcript views

23 Ensembl stable IDs ENSG########### ENST########### ENSP########### ENSE########### Ensembl Gene ID Ensembl Transcript ID Ensembl Peptide ID Ensembl Exon ID For non-human species a suffix is added: MUS (Mus musculus) for mouse ENSMUSG### DAR (Danio rerio) for zebrafish: ENSDARG###

24 Why Gene Ontology (GO)? Multiple terms for the same thing Gene descriptions too specific Non-specific immunity Innate immunity Natural killer cells Cytokines Complement Phagocyte Mast cells

25 GO terms form a controlled vocabulary GO: innate immune response Innate immune responses are defense responses mediated by germline encoded components that directly recognise components of potential pathogens.

26 GO terms are hierarchical GO: immune response GO: GO: innate immune response complement activation, alternative pathway GO: hemolymph coagulation GO: induced systemic resistance GO: MAPK cascade involved in innate immune response GO: defence response, incompatible interaction GO: GO: GO: GO: response to type II interferon complement activation, lectin pathway innate immune response in mucosa virus induced gene silencing GO: GO: GO: GO: response to type I interferon melanisation defence response natural killer cell mediated immunity response to interferon-gamma GO: GO: GO: GO: positive reg of innate immune response plant-type hypersensitive response negative reg of innate immune response regulation of innate immune response

27 Questions?

28 Variation EBI is an Outstation of the European Molecular Biology Laboratory.

29 Variant sources

30 Variant types 1) Small scale in one or few nucleotides of a gene Small deletions and insertions (DIPs or indels) Single nucleotide polymorphism (SNP) A G A C T T G A C C T G T C T - A A C T G G A T G A C T T G A C - T G T C T G A A C G G G A 2) Large scale (>50bp) in chromosomal structure (structural variant) Copy number variants (CNV) Large deletions/duplications, insertions, translocations deletion duplication insertion translocation

31 Variant consequences CODING Synonymous Regulatory CODING Missense AAAAAAA ATG 5 Upstream 5 UTR Splice site Intronic 3 UTR 3 Downstream

32 SO consequence terms

33 Reference alleles BL102 AL476 BL BL102 AGTCGTAGCTAGC TAGGCCATAGGCGA AL CM553 CM IM768 IM Frequency T = 0.05, frequency G = 0.95 G is the allele in all primates T causes disease susceptibility T is allele in the contig used so T is the reference allele and G is the alternate allele and alleles are T/G

34 Allele strand AGTCGTAGCTAGC T/GAGGCCATAGGCGA TCGCCTATGGCCT A/CGCTAGCTACGACT Exon sequence: TATGGCCTA/CGCTAGC Alleles in database = T/G Alleles in gene = A/C Alleles = A/C -ve strand or T/G +ve strand Alleles = A/C or T/G Often lack further info

35 Questions?

36 Help and documentation Course online Tutorials Videos us

37 Host a FREE Workshop! Invite one of our outreach team to teach at your institution for free (except trainer s expenses) us: helpdesk@ensembl.org Browser Course ½-2 day course on the Ensembl browser, aimed at wet-lab scientists. 1-2 trainers. API course 2-4 day course on the Ensembl APIs (Perl or REST) aimed at bioinformaticians. 1-4 trainers.

38 Acknowledgements The Entire Ensembl Team Funding Co-funded by the European Union

39 Training materials Ensembl training materials are protected by a CC BY license If you wish to re-use these materials, please credit Ensembl for their creation If you use Ensembl for your work, please cite our papers s.html