1 / 32

How to access genomic information using Ensembl

Learn how to access genomic information using Ensembl, a public website that offers annotation and links to automated genomic sequence assemblies. Explore genes, variations, and functional annotations across different species.

margaretrice
Télécharger la présentation

How to access genomic information using Ensembl

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. How to access genomic information using Ensembl August 2005

  2. GOAL

  3. Status of the human sequence finished red /orange ~96% (99.999% accurate) 30-40% repetitive elements (eg Alpha satellite, Alu repeats) All known genes, correctly identified (99.74%) heterochromatin ~4% grey Assembled draft sequence totals 2.85 Gb

  4. Finishing the euchromatic sequence of the human genome, Nature 431:931-45 (2004)

  5. SNP Manual Annotation Ensembl Supporting Databases Final DB Analysis DB CPU

  6. Genome browsingwhy present the whole genome? • Explore what is in a chromosome region • See features in and around a specific gene • Search & retrieve across the whole genome • Investigate genome organization • Compare to other genomes

  7. Ensembl – public site + installable system http://www.ensembl.org http://www.ncbi.nlm.nih.gov/mapview http://genome.ucsc.edu Genome browsers • UCSC Human Genome Browser • NCBI Map Viewer

  8. Introduction to the Ensembl web site Ensembl … … takes genomic sequence assemblies human build 35, mouse, rat, mosquito… adds annotation and links automated process presents all the data on a web site

  9. Basic Genome Annotation • Genes • Genomic location • Gene model structures • Exons • Introns • UTRs • Transcript(s) • Pseudogenes • Non-coding RNA • Protein(s) • Links to other sources of information

  10. Advanced Genome Annotation • Cytogenetic bands • Polymorphic markers • Sequence Tagged Sites (STS) • Genetic variation • Single Nucleotide Polymorphisms (SNPs) • Deletion-Insertion Polymorphisms (DIPs) • Short Tandem Repeats (STRs) • Repetitive sequences • Expressed Sequence Tags (ESTs) • cDNAs or mRNAs from related species • Regions of sequence homology

  11. Species homepage Map View Text search BLAST SSAHA How to get started … …

  12. Homepage

  13. MapView

  14. See blast hit on genome BLAST and SSAHA

  15. BLAST and SSAHA practical Query sequence: http://genome.imim.es/~nlopez/UVIC/seq.fas Practical: In which chromosome you get the best hit? Explore the alignment of the query sequence with the genome Is this is a sequence of a gene? If so, which one? Explore the region around this sequence

  16. Regions, maps and markers ContigView CytoView SyntenyView MultiContigView MarkerView SNPView GeneSNPView

  17. EnsemblContigView

  18. ContigViewclose-up Transcripts red & black (Ensembl predictions) Blue (Vega) Pop-up menu

  19. ContigView - Chromosome 20 close-up Manual annotation via Vega Ensembl predictions Ensembl EST-based predictions Chromosomes with manual annotation (http://vega.sanger.ac.uk):1, 6, 7, 9, 10, 13, 14, 16, 18, 19, 20, 22, X and Y

  20. CytoView

  21. GeneSNPView

  22. SNPView

  23. MarkerView

  24. SyntenyView

  25. MultiContigView

  26. Genes & gene products GeneView TransView ExonView ProteinView FamilyView DomainView GOView DiseaseView

  27. EnsemblGeneView

  28. TransView ExonView

  29. ProteinView

  30. FamilyView

  31. GOView

  32. Ensembl practical • Type the name of your favorite gene (i.e. BRCA2) and explore all the sections of ensembl for this gene. • Has this gene an ortholog in mouse? • How many different transcript do we know of this gene? • How many exons has the longest transcript? • Which functional annotations has this gene? (hint: check at GO annotations • Can you find SNPs in this gene?

More Related