Overview of the comparative data available at VectorBase

1. Comparative data in VectorBase
Comparative data in VectorBase
Karyn Mégy
November 2008
2008-11 Karyn Mégy

2. Comparative data in VectorBase
• DNA/DNA comparisons
– Pairwise and multiple alignments
– Constrained elements between genomes
• Protein/protein comparisons
– Ortholog/Paralog calculation
– Gene Tree
• Synteny
– Accessible as raw data in the database
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3. Comparative data in VectorBase
• Comparative data was obtained by running the Ensembl Compara
pipeline:
http://www.ensembl.org/info/about/docs/compara/index.html
• Data is accessible from the ContigView and the GeneView pages.
– ContigView
http://www.ensembl.org/common/Workshops_Online?id=115
– GeneView
http://www.ensembl.org/common/Workshops_Online?id=113
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4. DNA/DNA comparison
• Pairwise comparison
– tBLAT between all VectorBase organisms
• Multiple alignments
– Pecan 3-way alignments for the mosquito genomes
• Constrained elements
- Highly conserved elements between the three mosquito genomes
=> Accessible through ContigView pages
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5. ContigView: displaying comparative data
Comparative data tracks are not switched on by
default, so you will need to switch them on:
3.
2.
1. On the ContigView page, 4.
2. In the ‘Detailed view’ section,
3. Under the ‘Comparative’ menu,
4. Select the tracks you wish to see,
5. Close the menu.
6. The page will refresh showing
the new tracks selected.
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6. tBLAT alignments
Switch on the ‘tBLAT’ tracks in the
‘Comparative’ menu of the ‘DetailedView’
section
The pink rectangles indicate
similarity between the reference
genome (in this case Anopheles
gambiae) and Drosophila
melanogaster [Dmel],
Culex quinquefasciatus [Cpip],
and Aedes aegypti [Aaeg].
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7. tBLAT: Exploring the alignments
Select one of the pink rectangles to…
… jump to another genome,
… view a dot plot (‘dotter’),
… jump to a MultiContigView,
… view alignments.
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8. Multiple alignments and constrained elements
Select the ‘Pecan’ and ‘Constrained
elements’ tracks in the ‘Comparative’ menu
Highly conserved
elements between
the three mosquito
genomes
Similarities between
the three mosquito
genomes
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9. PECAN: exploring the alignments
Select the brown or pale pink rectangles to…
… jump to another genome,
… jump to the AlignSliceView
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10. PECAN: exploring the alignments
… jump to another genome … jump to the AlignSliceView
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11. Protein/protein comparison
• Orthologs and paralogs
– Orthologs between the VectorBase organisms, plus
Drosophila, Human and C. elegans
– Paralogs within species, for the VectorBase organisms
and Drosophila, Human and C. elegans
• Gene Tree
- Visualisation of the gene families
=> Accessible through GeneView pages
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12. Orthologs/paralogs
In the GeneView page
1. Select the orthologs/paralogs to
view the GeneView page for these
genes
2. Select the ‘MultiContigView’
to see both genes together
3. Select ‘Align’ to see peptide
1. 2. 3.
alignments (in various formats)
4. 4. Select ‘View alignment of
Homologies’ to see all the
pairwise alignments
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13. Orthologs/paralogs: Exploring
1. ‘GeneView’ 2. ‘MultiContigView’
ortholog
DNA
similarities
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14. Orthologs/paralogs: Exploring
3. Alignment (various formats)
4. Pairwise alignments
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15. GeneTrees
On the GeneView page, in the left hand menu:
The GeneTree
summarises the
relationships in this
gene family
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16. More information?
* E-mail VectorBase curators at info@vectorbase.org
* Post a question on the forum
http://www.vectorbase.org/sections/Forum/index.php
* Check out the Frequently Asked Questions (FAQ)
http://www.vectorbase.org/Help/Help:Contents
2008-11 Karyn Mégy