This document provides an overview of genome browsing at VectorBase, an online genomic database for invertebrate vectors of human pathogens. It describes the species available, data types, and how to navigate the main page and genome browser. Key features of the genome browser include viewing genomic regions at different levels of detail, searching or browsing to genes of interest, and adding custom tracks with additional data. Help documentation is also available.

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