Comparative data in VectorBase




         Comparative data in VectorBase

                      Karyn Mégy
             ...
Comparative data in VectorBase


•   DNA/DNA comparisons
     – Pairwise and multiple alignments
     – Constrained elemen...
Comparative data in VectorBase


•   Comparative data was obtained by running the Ensembl Compara
    pipeline:
       htt...
DNA/DNA comparison


•    Pairwise comparison
      – tBLAT between all VectorBase organisms
•    Multiple alignments
    ...
ContigView: displaying comparative data


   Comparative data tracks are not switched on by
     default, so you will need...
tBLAT alignments



                     Switch on the ‘tBLAT’ tracks in the
                     ‘Comparative’ menu of th...
tBLAT: Exploring the alignments


Select one of the pink rectangles to…




                                        … jump...
Multiple alignments and constrained elements


                      Select the ‘Pecan’ and ‘Constrained
                 ...
PECAN: exploring the alignments


Select the brown or pale pink rectangles to…




                                       ...
PECAN: exploring the alignments

… jump to another genome     … jump to the AlignSliceView




 2008-11 Karyn Mégy        ...
Protein/protein comparison


•   Orthologs and paralogs
     – Orthologs between the VectorBase organisms, plus
       Dro...
Orthologs/paralogs

In the GeneView page
                                 1. Select the orthologs/paralogs to
            ...
Orthologs/paralogs: Exploring




       1. ‘GeneView’      2. ‘MultiContigView’




                                     ...
Orthologs/paralogs: Exploring


        3. Alignment (various formats)




4. Pairwise alignments




2008-11 Karyn Mégy  ...
GeneTrees

On the GeneView page, in the left hand menu:




       The GeneTree
       summarises the
       relationships...
More information?




  * E-mail VectorBase curators at info@vectorbase.org

  * Post a question on the forum
       http:...
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VectorBase Comparative data

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Overview of the comparative data available at VectorBase

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VectorBase Comparative data

  1. 1. Comparative data in VectorBase Comparative data in VectorBase Karyn Mégy November 2008 2008-11 Karyn Mégy
  2. 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 2008-11 Karyn Mégy 2
  3. 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 2008-11 Karyn Mégy 3
  4. 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 2008-11 Karyn Mégy 4
  5. 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. 2008-11 Karyn Mégy 5
  6. 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]. 2008-11 Karyn Mégy 6
  7. 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. 2008-11 Karyn Mégy 7
  8. 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 2008-11 Karyn Mégy 8
  9. 9. PECAN: exploring the alignments Select the brown or pale pink rectangles to… … jump to another genome, … jump to the AlignSliceView 2008-11 Karyn Mégy 9
  10. 10. PECAN: exploring the alignments … jump to another genome … jump to the AlignSliceView 2008-11 Karyn Mégy 10
  11. 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 2008-11 Karyn Mégy 11
  12. 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 2008-11 Karyn Mégy 12
  13. 13. Orthologs/paralogs: Exploring 1. ‘GeneView’ 2. ‘MultiContigView’ ortholog DNA similarities 2008-11 Karyn Mégy 13
  14. 14. Orthologs/paralogs: Exploring 3. Alignment (various formats) 4. Pairwise alignments 2008-11 Karyn Mégy 14
  15. 15. GeneTrees On the GeneView page, in the left hand menu: The GeneTree summarises the relationships in this gene family 2008-11 Karyn Mégy 15
  16. 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
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