2008-11 Karyn Mégy

Comparative data in VectorBase

Karyn MégyNovember 2008

Comparative data in VectorBase

22008-11 Karyn Mégy

• 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

Comparative data in VectorBase

32008-11 Karyn Mégy

• Comparative data was obtained by running the Ensembl Comparapipeline:

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

Comparative data in VectorBase

42008-11 Karyn Mégy

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

52008-11 Karyn Mégy

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

ContigView: displaying comparative data

1. On the ContigView page,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 showingthe new tracks selected.

3.2.

4.

62008-11 Karyn Mégy

tBLAT alignments

The pink rectangles indicatesimilarity between the referencegenome (in this case Anophelesgambiae) and Drosophilamelanogaster [Dmel],Culex quinquefasciatus [Cpip],and Aedes aegypti [Aaeg].

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

72008-11 Karyn Mégy

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.

82008-11 Karyn Mégy

Multiple alignments and constrained elements

Select the ‘Pecan’ and ‘Constrainedelements’ tracks in the ‘Comparative’ menu

Similarities betweenthe three mosquitogenomes

Highly conservedelements betweenthe three mosquitogenomes

92008-11 Karyn Mégy

PECAN: exploring the alignments

Select the brown or pale pink rectangles to…

… jump to another genome,… jump to the AlignSliceView

102008-11 Karyn Mégy

… jump to another genome … jump to the AlignSliceView

PECAN: exploring the alignments

112008-11 Karyn Mégy

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

122008-11 Karyn Mégy

Orthologs/paralogs

In the GeneView page

1. Select the orthologs/paralogs toview the GeneView page for thesegenes

2. Select the ‘MultiContigView’to see both genes together

3. Select ‘Align’ to see peptidealignments (in various formats)

4. Select ‘View alignment ofHomologies’ to see all thepairwise alignments

1. 2. 3.

4.

132008-11 Karyn Mégy

2. ‘MultiContigView’

orthologDNA

similarities

Orthologs/paralogs: Exploring

1. ‘GeneView’

142008-11 Karyn Mégy

3. Alignment (various formats)

4. Pairwise alignments

Orthologs/paralogs: Exploring

152008-11 Karyn Mégy

GeneTrees

On the GeneView page, in the left hand menu:

The GeneTreesummarises therelationships in thisgene family

2008-11 Karyn Mégy

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