VectorBase
http://www.vectorbase.org




               Comparative data in VectorBase

                            Novemb...
VectorBase
   http://www.vectorbase.org




                        Comparative data in VectorBase

       • DNA/DNA compa...
VectorBase
   http://www.vectorbase.org




                        Comparative data in VectorBase

       • Comparative d...
VectorBase
   http://www.vectorbase.org




                               DNA/DNA comparison

       • Pairwise compariso...
VectorBase
   http://www.vectorbase.org




           ContigView: displaying the comparative data

       • Comparative d...
VectorBase
   http://www.vectorbase.org




           ContigView: displaying the comparative data

       • And you get:
...
VectorBase
   http://www.vectorbase.org




                                   tBLAT


                               Swit...
VectorBase
   http://www.vectorbase.org




                                      tBLAT

   Click on one of the pink recta...
VectorBase
   http://www.vectorbase.org




                          Multiple alignments (PECAN)
                        ...
VectorBase
   http://www.vectorbase.org




                          Multiple alignments (PECAN)
                        ...
VectorBase
   http://www.vectorbase.org


      … jump on the other genomes   … see the AlignSliceView




Karyn Mégy -Nov...
VectorBase
   http://www.vectorbase.org




                               Protein/protein comparison

       • Orthologs ...
VectorBase
   http://www.vectorbase.org




                                    Orthologs/paralogs
   In the GeneView page...
VectorBase
   http://www.vectorbase.org



            2. ‘MultiContigView’                3. Alignment (various formats)
...
VectorBase
   http://www.vectorbase.org




                                   GeneTree

   On the GeneView page, in the l...
VectorBase
http://www.vectorbase.org




                                Questions?


                        * E-mail inf...
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Comparative data in VectorBase

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

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Comparative data in VectorBase

  1. 1. VectorBase http://www.vectorbase.org Comparative data in VectorBase November 2008
  2. 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. 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. 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. 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. 6. VectorBase http://www.vectorbase.org ContigView: displaying the comparative data • And you get: Karyn Mégy -November 2008 6
  7. 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. 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. 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. 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. 11. VectorBase http://www.vectorbase.org … jump on the other genomes … see the AlignSliceView Karyn Mégy -November 2008 11
  12. 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. 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 Karyn Mégy -November 2008 13
  14. 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. 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. 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

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