Comparative data in VectorBase

http://www.vectorbase.org

VectorBase

Comparative data in VectorBase

November 2008

Karyn Mégy -November 2008 2


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




VectorBase

• Comparative data was generated by running theEnsembl Compara pipeline :

http://www.ensembl.org/info/about/docs/compara/index.html

• Accessible from the ContigView[1] and theGeneView[2] pages, as well as from the left handmenu 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



VectorBase

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



VectorBase

• Comparative data tracks are not switched on bydefault, so you will need to switch them on:

ContigView: displaying the comparative data

1. In the Contig View,2. In the ‘Detailed View’ section,3. Under the ‘Comparative’ menu,4. Select the tracks you want to see,5. Close the menu6. The new tracks will appear.

3.2.

4.



VectorBase

• And you get:

ContigView: displaying the comparative data



VectorBase

tBLAT

The pink rectangles indicates thesimilarities between Anophelesand Drosophila [track A],Culex [track B],and Aedes [track C].

[B][C]

[A]

Switch on the ‘tBLAT’ tracks in the ‘Comparative’menu of the ‘DetailedView’ section



VectorBase

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.



VectorBase

Multiple alignments (PECAN)and constrained elements

Switch on the ‘Pecan’ and ‘Constrained elements’tracks in the ‘Comparative’ menuof the ‘DetailedView’ section

Similarities betweenthe 3 mosquitoes

Highly conservedelements betweenthe 3 mosquitoes



VectorBase

Multiple alignments (PECAN)and constrained elements

Click on the brown or pale pink rectangles to…

… see the AlignSliceView,… jump to the other genomes.



VectorBase

… jump on the other genomes … see the AlignSliceView



VectorBase

Protein/protein comparison

• Orthologs and paralogs– Orthologs between all the VectorBase organisms,

plus Drosophila, Human and C.elegans

– Paralogs within species, for all the VectorBaseorganisms, plus Drosophila, Human and C.elegans

• Gene Tree- Visualisation of the gene families

=> Accessible from GeneView



VectorBase

Orthologs/paralogs

In the GeneView page

1. Click on the orthologs/paralogsto see the GeneView page of thesegenes.

2. Click on ‘MultiContigView’to see both genes in this view

3. Click on ‘Align’ to see thealignment (in various formats)

4. Click on ‘View alignment ofHomologies’ to see all the pairwisealignments

1. 2. 3.

4.



VectorBase

2. ‘MultiContigView’ 3. Alignment (various formats)

4. All the pairwise alignments

orthologDNA

similarities



VectorBase

GeneTree

On the GeneView page, in the left hand menu:

The GeneTree summarisesthe relationships in thisgene family


VectorBase

Questions?

* E-mail [email protected]* 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

Comparative data in VectorBase

Technology

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