Ensembl Plants: Visualising, mining and analysing crop genomics data

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Ensembl Plants is a genome centric platform for visualisation and analysis of plant genomics data. It hosts assembly, sequence, expression, variation and comparative datasets for a growing number of plant species (currently 26) covering a range of economically important crops, including brassica, tomato, grape, barley, potato, maize and wheat, and taxonomically diverse model organisms. The web-based genome browser visually integrates sequence and assembly information with genes, markers, probes, repeats and other public or user-supplied datasets. It includes a web-based data mining tool, allowing specific sets of data to be queried and downloaded for offline analysis. In addition to the browser, all data can be accessed computationally via extensive Perl and REST APIs and is available for FTP download or direct database access.

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Ensembl Plants: Visualising, mining and analysing crop genomics data

  1. 1. Ensembl Plants: Visualising, mining and analysing crop genomics data Dan Bolser Ensembl Plants project leader EMBL-EBI http://plants.ensembl.org #EnsemblGenomes
  2. 2. Visualising, mining and analysing data: ● The Ensembl genome browser ● BioMart ● Tools for processing your own data Overview Background: ● Ensembl Plants ● History ● Data ● Recent updates ● Wheat ● Barley
  3. 3. EBI Ensembl is developed jointly by the EBI and the Wellcome Trust Sanger Institute
  4. 4. Ensembl Plants uses Ensembl technology Ensembl: ● A platform for genome browsing, annotation and analysis developed jointly by the EBI and Wellcome Trust Sanger Institute. ● Has modules for handling: ● Genomic data, Variations, Comparative genomics, Gene prediction, ... ● Multiple points of access to data: ● Browser-based application, Perl and REST APIs, direct access (MySQL), BioMart data mining tool, DAS (client and server), FTP. ● Upload your own data and compare it to the reference seq. and annotation. Ensembl was originally developed for vertebrate genomes, subsequently extended to non-vertebrate species: ● Ensembl Genomes → Ensembl Plants
  5. 5. Currently 33 genomes in Ensembl Plants http://plants.ensembl.org
  6. 6. Dicots in Ensembl Plants (10) Brassicales Fabales Malpighiales Rosales Solanales Vitales
  7. 7. Monocots in Ensembl Plants (12+5) Poales Zingiberales
  8. 8. 'Others' (5)
  9. 9. Types of data in Ensembl (Ensembl Plants) ● Genomic sequence ● Gene, transcript, and protein annotations ● External references and ontology terms ● Mapped sequences: cDNAs, proteins, probes, BACs, repeats, markers, ... ● Variation data: ● sequence variants ● structural variants ● Comparative data: ● gene trees, orthologues, paralogues ● whole genome alignments and synteny
  10. 10. Recent data updates
  11. 11. Wheat data in Ensembl Plants ● The chromosome survey sequence from the International Wheat Genome Sequencing Consortium. ● Version 2.1 of the IWGSC gene models called on the chromosome survey sequence. ● Repeats ● Repbase ● The Triticeae Repeat Sequence Database (TREP) ● Alignments ● RNA-seq from various studies in ENA ● ESTs and UniGene clusters ● 5x 454 Brenchley et al. ● Triticum turgidum cDNA assemblies
  12. 12. Wheat data in Ensembl Plants ● Whole genome alignments ● Between wheat(s) and: ● Rice ● Brachypodium ● Within wheat ● A vs. B ● A vs. D ● B vs. D ● Gene trees ● Aegilops tauschii ● Triticum urartu ● and other more distant relatives
  13. 13. WGA between wheat, rice and brachy
  14. 14. WGA within wheat A, B and D sub-genomes
  15. 15. Gene trees
  16. 16. Gene trees
  17. 17. Walk through ‘demo’ for Ensembl Plants
  18. 18. Search
  19. 19. Variant Effect Predictor (VEP) ● Predicts functional consequences of known and unknown variants ● For substitutions, insertions, deletions and structural variants ● Web interface (for up to 750 variants), standalone Perl script, Perl API and REST API
  20. 20. Visualise your own data Upload data: ● Data saved on server ● 5 MB limit ● Large file formats? Attach remote files: ● URL-based ● HTTP or FTP ● No size limit Upload formats: ● BED genes / features ● Gbrowse genes / features ● GFF/GTF genes / features ● PSL sequence alignments ● WIG continuous-valued data ● BedGraph continuous-valued data ● TrackHub collections of tracks Attach formats: ● BigBed genes / features ● BAM sequence alignments ● BigWig continuous-valued data ● VCF variants User added tracks: ● Can be saved or shared ● Only trivial security, do not use for sensitive data!
  21. 21. The barley Gene-ome
  22. 22. ● Step 1 – Dataset ● Choose your dataset and species ● Step 2 – Filters ● Limit your dataset ● Step 3 – Attributes ● Specify what information you want to output ● Step 4 – Results ● Preview and output your results Blast and BioMart...
  23. 23. pkersey@ebi.ac.uk10/01/2014 Funding (Ensembl Plants) • Ensembl Genomes Funded by • EMBL • EU (INFRAVEC, Microme, transPLANT, AllBio) • BBSRC (PhytoPath, wheat, barley and midge sequencing, UK-US collaboration, RNAcentral) • Wellcome Trust (PomBase) • NIH/NIAID (VectorBase) • NSF (Gramene collaboration) • Bill and Melinda Gates Foundation (wheat rust)
  24. 24. pkersey@ebi.ac.uk10/01/2014 People (Ensembl Plants) • James Allen, Irina Armean, Dan Bolser, Mikkel Christensen, Paul Davies, Christoph Grabmueller, Kevin Howe, Malcolm Hinsley, Jay Humphrey, Arnaud Kerhornou, Paul Kersey, Julia Khobdova, Eugene Kulesha, Nick Langridge, Dan Lawson, Mark McDowall, Uma Maheswari, Gareth Maslen, Michael Nuhn, Chuang Kee Ong, Michael Paulini, Helder Pedro, Anton Petrov, Dan Staines, Mary Ann Tuli, Brandon Walts, Gary Williams • If you have a question that is not answered here, please Contact our HelpDesk: • helpdesk@ensemblgenomes.org

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