A quick introduction to comparative data in VectorBase: how to find orthologues, paralogues, synteny, DNA alignments

1. VectorBase
http://www.vectorbase.org
Comparative data in VectorBase
Karyn Mégy & Dan Lawson
Updated May 2010
Karyn Mégy Dan Lawson – May 2010 1

2. VectorBase
http://www.vectorbase.org
Comparative data in VectorBase
• DNA/DNA comparison
– Pairwise and multiple alignments
– Constrained elements
• Protein/protein comparison
– Orthologues/Paralogues
– Gene Trees
• Synteny
– Accessible as raw data in the database
Karyn Mégy Dan Lawson – May 2010 2

3. VectorBase
http://www.vectorbase.org
Comparative data in VectorBase
• Comparative data was generated by running the
Ensembl GeneTree pipeline:
http://www.ensembl.org/info/docs/compara/homology_method.html
Vilella et al. Genome Res. 2009. PMID: 19029536
• Accessible from the left hand menu in the Location
or Gene tabs (see next slide)
• Data type availability depends on the species
(e.g.: DNA data only available for close species, such as mosquitoes)
Karyn Mégy Dan Lawson – May 2010 3

4. VectorBase
http://www.vectorbase.org
Accessing the comparative data
Gene tab
Location tab
Karyn Mégy Dan Lawson – May 2010 4
4

5. VectorBase
http://www.vectorbase.org
DNA/DNA comparison between genomes
• 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 the Location Tab
Karyn Mégy Dan Lawson – May 2010 5

6. VectorBase
http://www.vectorbase.org
Location tab
• Four items:
[1] Graphical view of the
alignment,
[2] Text view of the
alignment,
[3] Multi-species alignment,
[4] Synteny view
Karyn Mégy Dan Lawson – May 2010 6

7. VectorBase
http://www.vectorbase.org
[1] Graphical view of the alignment
1- Click on
“Alignments (image)”
1.
2- Select the alignment
type in the menu
Note that what’s in the menu
2.
depends on the data
available for the species.
The example here is
Anopheles gambiae.
Karyn Mégy Dan Lawson – May 2010 7

8. VectorBase
http://www.vectorbase.org
tBLAT
Karyn Mégy Dan Lawson – May 2010 8

9. VectorBase
http://www.vectorbase.org
tBLAT
Black = breakpoint
Red = gap
Blue = inversion
• Clicking on an arrow gives
you details about alignment
breaks
• Clicking on a gene gives
you information about the
gene (and even allows you to
‘jump’ to another species)
Karyn Mégy Dan Lawson – May 2010 9

10. VectorBase
http://www.vectorbase.org
tBLAT
2.
1.
• On this panel you can:
1- Change positions,
2- Zoom in/out,
3- Export the page
3.
Karyn Mégy Dan Lawson – May 2010 10

11. VectorBase
http://www.vectorbase.org
[2] Text view of the alignment
1- Click on
“Alignments (text)”
2- Select the alignment
1.
type in the menu
2.
Note that what’s in the menu
depends on the data
available for the species.
The example here is
Anopheles gambiae.
Karyn Mégy Dan Lawson – May 2010 11

12. VectorBase
http://www.vectorbase.org
[2] Text view of the alignment
2.
1.
• On this panel you can:
1- Change positions,
3.
2- Zoom in/out,
3- ‘Jump’ to another species
Note: have you seen you
can get on-line Help?
Karyn Mégy Dan Lawson – May 2010 12

13. VectorBase
http://www.vectorbase.org
[3] Multi-species alignment
1- Click on
“Multi-species view”
2- Select the alignment
type in the menu
1.
2.
Note that what’s in the menu
depends on the data
available for the species.
The example here is
Anopheles gambiae.
Karyn Mégy Dan Lawson – May 2010 13

14. VectorBase
http://www.vectorbase.org
[3] Multi-species alignment
1.
1.
2.
• FIRST panel:
1- ‘Jump’ to another species (by clicking on its gene or selecting a region)
2- Export data from this region
Note: have you seen you
can get on-line Help?
Karyn Mégy Dan Lawson – May 2010 14

15. VectorBase
http://www.vectorbase.org
[3] Multi-species alignment
1.
2.
3.
3.
• SECOND panel:
4.
1- Change positions,
2- Zoom in/out,
3- ‘Jump’ to another species (by clicking on its gene or selecting a region),
4- Export data from this region
Karyn Mégy Dan Lawson – May 2010 15

16. VectorBase
http://www.vectorbase.org
Protein / protein comparison
• Orthologs and paralogs
– Orthologs between all the VectorBase organisms,
+ D.melanogaster and C.elegans
– Paralogs within/between species, for all the
VectorBase organisms, + D.melanogaster
and C.elegans
• Gene Tree
- Visualisation of the gene families
= accessible from the Gene Tab
Karyn Mégy Dan Lawson – May 2010 16

17. VectorBase
http://www.vectorbase.org
Gene tab
• Five items:
[1] Genomic alignments,
[2] Gene Trees,
[3] Orthologues,
[4] Paralogues,
[5] Protein families
(not necessarily available)
Karyn Mégy Dan Lawson – May 2010 17

18. VectorBase
http://www.vectorbase.org
[1] Genomic alignments
1- Click on
“Genomic Alignments”
2- Select the alignment
type in the menu
1.
2.
Karyn Mégy Dan Lawson – May 2010 18

19. VectorBase
http://www.vectorbase.org
[1] Genomic alignments
• On this panel you can:
– Change species for alignment,
– Go to a graphical view,
– ‘Jump’ to another species
Karyn Mégy Dan Lawson – May 2010 19

20. VectorBase
http://www.vectorbase.org
[2] Gene Tree – type selection
• Select GeneTree type:
• image,
• text,
• alignment
Karyn Mégy Dan Lawson – May 2010 20

21. VectorBase
http://www.vectorbase.org
1.
[2] Gene Tree (image)
2.
4.
3.
• On this panel you can:
1- Expand the tree (by clicking on the nodes),
2- Get more information on a sub-tree,
3- Change the views,
4- Export the image
Note: have you seen you
can get on-line Help?
Karyn Mégy Dan Lawson – May 2010 21

22. VectorBase
http://www.vectorbase.org
2.
[2] GeneTree (text)
• In this panel you can:
1- Get the tree in Newick
1.
format,
2- Change the format by
selecting
“configure this page”
Formats: Newick
NHX, text
Note: have you seen you
can get on-line Help?
Karyn Mégy Dan Lawson – May 2010 22

23. VectorBase
http://www.vectorbase.org
2.
[2] GeneTree (alignment)
• In this panel you can:
1- Get the alignment in MSF
1.
format,
2- Change the format by
selecting
“configure this page”
Formats: MSF, Clustal, Fasta
Mega, Nexus, PSI
Pfam, Phylip, Selex
Note: have you seen you
can get on-line Help?
Karyn Mégy Dan Lawson – May 2010 23

24. VectorBase
http://www.vectorbase.org
[34] Orthologues/Paralogues
• Select orthologues or
paralogues
• Number of orthologues/
paralogues indicated in
parenthesis
Here, the gene CPR41 has:
• 4 orthologues,
• 6 paralogues
Karyn Mégy Dan Lawson – May 2010 24

25. VectorBase
http://www.vectorbase.org
[3] Orthologues
1.
• In this panel you can:
2.
1- ‘jump’ to another species
2- see the protein pairwise alignment (2 way)
Note: have you seen you
can get on-line Help?
Karyn Mégy Dan Lawson – May 2010 25

26. VectorBase
http://www.vectorbase.org
[4] Paralogues
1.
3.
• In this panel you can:
1- ‘jump’ to another species,
2- See the protein pairwise
alignment (2 way),
3- See the alignment of both
genomic regions (image)
2.
Note: have you seen you
can get on-line Help?
Karyn Mégy Dan Lawson – May 2010 26

27. 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
* Look in the Ensembl documentation
http://www.ensembl.org/info/docs/compara/index.html
Karyn Mégy Dan Lawson – May 2010 27