Description of the comparative data hosted at VectorBase (generation, accessibility)

1. VectorBase
http://www.vectorbase.org
Comparative data in VectorBase
November 2008

2. VectorBase
http://www.vectorbase.org
Comparative data in VectorBase
• DNA/DNA comparison
– Pairwise and multiple alignments
– Constrained elements
• Protein/protein comparison
– Orthologs/Paralogs
– Gene Tree
• Synteny
– Accessible as raw data in the database
Karyn Mégy -November 2008 2

3. VectorBase
http://www.vectorbase.org
Comparative data in VectorBase
• Comparative data was generated by running the
Ensembl Compara pipeline :
http://www.ensembl.org/info/about/docs/compara/index.html
• Accessible from the ContigView[1] and the
GeneView[2] pages, as well as from the left hand
menu of the GeneView page.
[1] ContigView: http://www.ensembl.org/common/Workshops_Online?id=115
[2] GeneView: http://www.ensembl.org/common/Workshops_Online?id=113
Karyn Mégy -November 2008 3

4. VectorBase
http://www.vectorbase.org
DNA/DNA comparison
• Pairwise comparison
– tBLAT between all the VectorBase organisms
• Multiple alignments
– Pecan 3-way alignments for the three mosquito
genomes
• Constrained elements
- Highly conserved elements between the three
mosquitoes
=> Accessible from ContigView
Karyn Mégy -November 2008 4

5. VectorBase
http://www.vectorbase.org
ContigView: displaying the comparative data
• Comparative data tracks are not switched on by
default, so you will need to switch them on:
3.
2.
1. In the Contig View, 4.
2. In the ‘Detailed View’ section,
3. Under the ‘Comparative’ menu,
4. Select the tracks you want to see,
5. Close the menu
6. The new tracks will appear.
Karyn Mégy -November 2008 5

6. VectorBase
http://www.vectorbase.org
ContigView: displaying the comparative data
• And you get:
Karyn Mégy -November 2008 6

7. VectorBase
http://www.vectorbase.org
tBLAT
Switch on the ‘tBLAT’ tracks in the ‘Comparative’
menu of the ‘DetailedView’ section
The pink rectangles indicates the
[A]
similarities between Anopheles
[B] and Drosophila [track A],
[C]
Culex [track B],
and Aedes [track C].
Karyn Mégy -November 2008 7

8. VectorBase
http://www.vectorbase.org
tBLAT
Click on one of the pink rectangles to…
… jump on the other genomes,
… see the dot plots (‘dotter’),
… see the MultiContigView,
… see the alignments.
Karyn Mégy -November 2008 8

9. VectorBase
http://www.vectorbase.org
Multiple alignments (PECAN)
and constrained elements
Switch on the ‘Pecan’ and ‘Constrained elements’
tracks in the ‘Comparative’ menu
of the ‘DetailedView’ section
Highly conserved
elements between
the 3 mosquitoes
Similarities between
the 3 mosquitoes
Karyn Mégy -November 2008 9

10. VectorBase
http://www.vectorbase.org
Multiple alignments (PECAN)
and constrained elements
Click on the brown or pale pink rectangles to…
… see the AlignSliceView,
… jump to the other genomes.
Karyn Mégy -November 2008 10

11. VectorBase
http://www.vectorbase.org
… jump on the other genomes … see the AlignSliceView
Karyn Mégy -November 2008 11

12. VectorBase
http://www.vectorbase.org
Protein/protein comparison
• Orthologs and paralogs
– Orthologs between all the VectorBase organisms,
plus Drosophila, Human and C.elegans
– Paralogs within species, for all the VectorBase
organisms, plus Drosophila, Human and C.elegans
• Gene Tree
- Visualisation of the gene families
=> Accessible from GeneView
Karyn Mégy -November 2008 12

13. VectorBase
http://www.vectorbase.org
Orthologs/paralogs
In the GeneView page
1. Click on the orthologs/paralogs
to see the GeneView page of these
genes.
2. Click on ‘MultiContigView’
to see both genes in this view
3. Click on ‘Align’ to see the
1. 2. 3.
alignment (in various formats)
4. 4. Click on ‘View alignment of
Homologies’ to see all the pairwise
alignments
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14. VectorBase
http://www.vectorbase.org
2. ‘MultiContigView’ 3. Alignment (various formats)
ortholog
DNA
similarities
4. All the pairwise alignments
Karyn Mégy -November 2008 14

15. VectorBase
http://www.vectorbase.org
GeneTree
On the GeneView page, in the left hand menu:
The GeneTree summarises
the relationships in this
gene family
Karyn Mégy -November 2008 15

16. 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