Vb tutorial-genome browser2010

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  • 1. VectorBase http://www.vectorbase.org Genome Browsing at VectorBase Karyn Mégy May 2010 Karyn Mégy – May 2010 1
  • 2. VectorBase http://www.vectorbase.org Genome Browsing •  This tutorial will take you through: –  the list of data available (species/type), –  the information available from the main page, –  the entry points to the Genome Browser, –  the Genome Browser (location, gene & transcript tabs), –  adding a track with external data, –  how to search for help! Karyn Mégy – May 2010 2
  • 3. VectorBase http://www.vectorbase.org Species available •  Invertebrate Vectors of Human Pathogens only ! –  As of mid-2010: •  mosquitoes (Anopheles gambiae, Aedes aegypti, Culex quinquefasciatus), •  tick (Ixodes scapularis), •  body louse (Pediculus humanus) –  Coming next: •  Kissing bug (Rhodnius prolixus) •  Tsetse fly (Glossina morsitans) Karyn Mégy – May 2010 3
  • 4. VectorBase http://www.vectorbase.org Data types available •  Genomic sequences –  annotated with genes, transcripts, translations etc. –  mapped with proteins and ESTs •  Proteins from large scope of organisms (taxonomically grouped) and species-specific ESTs •  External references –  Link between the genes and other databases (e.g. Swissprot) Karyn Mégy – May 2010 4
  • 5. VectorBase http://www.vectorbase.org Genome Browsing •  This tutorial will take you through: –  the list of data available (species/type), –  the information available from the main page, –  the entry points to the Genome Browser, –  the Genome Browser (location, gene & transcript tabs), –  adding a track with external data, –  how to search for help! Karyn Mégy – May 2010 5
  • 6. VectorBase http://www.vectorbase.org Example •  Let’s take the example of Anopheles gambiae, •  chr. 2L : 39,221,590-39,222,203 •  Starting page: http://www.vectorbase.org/Anopheles_gambiae/Info/Index Karyn Mégy – May 2010 6
  • 7. VectorBase http://www.vectorbase.org Main page 4. •  From the main page: 1. 1- Search for a keyword, 3. 2- Access the genomes, 3- Have a glance at what’s new 2. in the latest release. 4- Access the BLAST, BioMart, FTP and help pages Karyn Mégy – May 2010 7
  • 8. VectorBase http://www.vectorbase.org Main page 1.  Search for a keyword –  Via popular genome, menu or complete list of species 2. Access the genomes –  in all species or in a given species 3. What’s new –  description of the latest improvements Karyn Mégy – May 2010 8
  • 9. VectorBase http://www.vectorbase.org Main page 4. Access other pages: –  BLAST: compare your sequence to the VectorBase sequences –  BioMart: sophisticated way to mine data and extract complex queries –  FTP: location to download data files –  Help pages: link to docs, help pages and FAQ Help! Blast BioMart FTP Karyn Mégy – May 2010 9
  • 10. VectorBase http://www.vectorbase.org Genome Browsing •  This tutorial will take you through: –  the list of data available (species/type), –  the information available from the main page, –  the entry points to the Genome Browser, –  the Genome Browser (location, gene & transcript tabs), –  adding a track with external data, –  how to search for help! Karyn Mégy – May 2010 10
  • 11. VectorBase http://www.vectorbase.org Entry points to the Genome Browser •  From the search box: –  Location, –  Gene or transcript names, –  Function •  Via the “sample entry points”: –  Location (karyotype, positions) –  Gene or transcript names, Karyn Mégy – May 2010 11
  • 12. VectorBase http://www.vectorbase.org Genome Browsing •  Once you’re in the Genome Browser, you see –  Location tab. –  Gene and transcript tabs. ! You need to have selected a gene to see the gene/ transcript tabs. •  You can navigate by using the left hand side menu or by clicking on the image itself Karyn Mégy – May 2010 12
  • 13. VectorBase http://www.vectorbase.org Genome Browsing •  This tutorial will take you through: –  the list of data available (species/type), –  the information available from the main page, –  the entry points to the Genome Browser, –  the Genome Browser (location, gene & transcript tabs), –  adding a track with external data, –  how to search for help! Karyn Mégy – May 2010 13
  • 14. VectorBase http://www.vectorbase.org Location Tab •  From here you can access: - various views for this region: - whole chromosome, - chromosome summary, - region overview, - region in details - comparative data, - genetic variation  & marker data (if available) •  You can also configure the page and visualise your own data. Karyn Mégy – May 2010 14
  • 15. VectorBase http://www.vectorbase.org Location Tab, the left hand side menu Region in detail Region overview Chromosome summary Whole genome Karyn Mégy – May 2010 15
  • 16. VectorBase http://www.vectorbase.org Location Tab •  3 zooms to view context as well as details Genes •  Default view: genes •  Visualise more data  (see later) Karyn Mégy – May 2010 16
  • 17. VectorBase http://www.vectorbase.org Location Tab, detailed view Scale Chr. band Scaffold name Location (move to another position/location) Genes Strand (+) DNA Features added Strand (-) by configuring the page (see later) Karyn Mégy – May 2010 17
  • 18. VectorBase http://www.vectorbase.org Location Tab, did you know? •  In this tab you can also: –  Export the image (button right), –  Zoom in or center on a specific region by  clicking at a position and dragging  the red window up to the desired location –  Click on a gene to get more information, and to access the GENE TAB Karyn Mégy – May 2010 18
  • 19. VectorBase http://www.vectorbase.org Gene Tab, the left hand side menu •  From here you can access: - gene data - alternative transcript, expression data - comparative genomic data, - orthologs, paralogs, gene tree - genetic variations  (if any available) - additional data - gene history (over releases) •  You can also configure the page and visualise your own data. Karyn Mégy – May 2010 19
  • 20. VectorBase http://www.vectorbase.org Gene Tab, the left hand side menu – gene information Supporting evidence Splice variant External references Jump from one view to the other via the menu or the ‘buttons’ Gene sequence Karyn Mégy – May 2010 20
  • 21. VectorBase http://www.vectorbase.org Gene Tab, the left hand side menu – comparative data Gene Tree Orthologues Alignments with other species  (C.quinquefasciatus in this case) Karyn Mégy – May 2010 21
  • 22. VectorBase http://www.vectorbase.org Transcript tab •  From here you can access: - transcript data •  … summary, supporting evidence, sequence, link to external databases - genetic variations  (if any available) - protein data summary, domains, variations - additional data •  You can also configure the page and visualise your own data. Karyn Mégy – May 2010 22
  • 23. VectorBase http://www.vectorbase.org Transcript tab the left hand side menu – transcript information Transcript data References to external DBs: External identifiers, probes, ontologies Sequences, Includes individual exons,  transcript and protein Karyn Mégy – May 2010 23
  • 24. VectorBase http://www.vectorbase.org Transcript tab the left hand side menu – protein information Protein domain visualisation Protein domain list Variation data, Listed only if a variation affects the protein, i.e. intronic variations are NOT listed in this section (see gene tab for those) Karyn Mégy – May 2010 24
  • 25. VectorBase http://www.vectorbase.org Genome Browsing •  This tutorial will take you through: –  the list of data available (species/type), –  the information available from the main page, –  the entry points to the Genome Browser, –  the Genome Browser (location, gene & transcript tabs), –  adding a track with external data, –  how to search for help! Karyn Mégy – May 2010 25
  • 26. VectorBase http://www.vectorbase.org Adding external data •  On the left hand side menu, for each of the tabs, there is a link to ‘manage your data’ or ‘export’ data: –  Data can be managed by: •  Adding pre-computed data that are not shown by default, •  Adding your own data (see DAS tutorial), Karyn Mégy – May 2010 26
  • 27. VectorBase http://www.vectorbase.org Adding external data •  Click on ’configure this page’: •  A pop-up window appears: Note: depending on the tab (‘location’ or ‘gene’) you’re in when selecting ‘configure this page’, the pop-up window will be different Karyn Mégy – May 2010 27
  • 28. VectorBase http://www.vectorbase.org Adding external data •  Select tracks and other options in the window, •  Close the popup window, •  The Genome Browser will be updated automatically. Note: To change whether a track is drawn OR how it is drawn, click on the icon by the track name to select the way the track will be drawn. Karyn Mégy – May 2010 28
  • 29. VectorBase http://www.vectorbase.org Genome Browsing •  This tutorial will take you through: –  the list of data available (species/type), –  the information available from the main page, –  the entry points to the Genome Browser, –  the Genome Browser (location, gene & transcript tabs), –  adding a track with external data, –  how to search for help! Karyn Mégy – May 2010 29
  • 30. VectorBase http://www.vectorbase.org Help! •  Multiple Help! points in the Genome Browser: 1- Help button in each view, 2- the pop-up window has documentation at the end, 3- docs and FAQ are available via the top right links, 4- … and you can always contact us via the bottom right link! 3. 1. Karyn Mégy – May 2010 2. 30 4.
  • 31. VectorBase http://www.vectorbase.org Questions? * E-mail info@vectorbase.org * Post your question on the forum http://www.vectorbase.org/sections/Forum/index.php * Check out the FAQs http://www.vectorbase.org/Help/Help:Contents * Ensembl Genome Browser tutorial http://www.ensembl.org/Help/Movie?id=188 Karyn Mégy – May 2010 31