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
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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
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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,
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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
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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
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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)
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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
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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
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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
