vb tutorial-compara-update2010

Karyn Mégy & Dan Lawson – May 2010 1

VectorBase http://www.vectorbase.org

Comparative data in VectorBase

Karyn Mégy & Dan Lawson��Updated May 2010



•  DNA/DNA comparison –  Pairwise and multiple alignments –  Constrained elements

•  Protein/protein comparison –  Orthologues/Paralogues –  Gene Trees

•  Synteny –  Accessible as raw data in the database




•  Comparative data was generated by running the Ensembl GeneTree pipeline:

http://www.ensembl.org/info/docs/compara/homology_method.html ��Vilella et al. Genome Res. 2009. PMID: 19029536

•  Accessible from the left hand menu in the Location or Gene tabs (see next slide)

•  Data type availability depends on the species ��(e.g.: DNA data only available for close species, such as mosquitoes)




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Accessing the comparative data

Location tab

Gene tab



•  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 the Location Tab

DNA/DNA comparison between genomes



Location tab

•  Four items: [1] Graphical view of the

alignment, [2] Text view of the

alignment, [3] Multi-species alignment, [4] Synteny view



[1] Graphical view of the alignment

1- Click on ��“Alignments (image)”

2- Select the alignment type in the menu

Note that what’s in the menu depends on the data available for the species. The example here is Anopheles gambiae.

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tBLAT



tBLAT

•  Clicking on an arrow gives you details about alignment breaks

•  Clicking on a gene gives ��you information about the gene (and even allows you to ‘jump’ to another species)

Black = breakpoint Red = gap Blue = inversion



tBLAT

•  On this panel you can: 1- Change positions, 2- Zoom in/out, 3- Export the page

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[2] Text view of the alignment

1- Click on ��“Alignments (text)”



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[2] Text view of the alignment

•  On this panel you can: 1- Change positions, 2- Zoom in/out, 3- ‘Jump’ to another species

Note: have you seen you can get on-line Help?

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[3] Multi-species alignment

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1- Click on ��“Multi-species view”






•  FIRST panel: 1- ‘Jump’ to another species (by clicking on its gene or selecting a region) 2- Export data from this region


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•  SECOND panel: 1- Change positions, 2- Zoom in/out, 3- ‘Jump’ to another species (by clicking on its gene or selecting a region), 4- Export data from this region

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Protein / protein comparison

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

+ D.melanogaster and C.elegans –  Paralogs within/between species, for all the

VectorBase organisms, + D.melanogaster ��and C.elegans

•  Gene Tree -  Visualisation of the gene families

=> accessible from the Gene Tab



Gene tab

•  Five items: [1] Genomic alignments, [2] Gene Trees, [3] Orthologues, [4] Paralogues, [5] Protein families ��

(not necessarily available)



[1] Genomic alignments

1- Click on ��“Genomic Alignments”


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[1] Genomic alignments

•  On this panel you can: –  Change species for alignment, –  Go to a graphical view, –  ‘Jump’ to another species



[2] Gene Tree – type selection

•  Select GeneTree type: •  image, •  text, •  alignment



[2] Gene Tree (image)

•  On this panel you can: 1- Expand the tree (by clicking on the nodes), 2- Get more information on a sub-tree, 3- Change the views, 4- Export the image Note: have you seen you

can get on-line Help?

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[2] GeneTree (text)

•  In this panel you can: 1- Get the tree in Newick

format, 2- Change the format by

selecting ��“configure this page”

Formats: Newick NHX, text


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[2] GeneTree (alignment)

•  In this panel you can: 1- Get the alignment in MSF

format, 2- Change the format by

selecting ��“configure this page”

Formats: MSF, Clustal, Fasta Mega, Nexus, PSI Pfam, Phylip, Selex


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[3&4] Orthologues/Paralogues

•  Select orthologues or paralogues

•  Number of orthologues/paralogues indicated in parenthesis

Here, the gene CPR41 has: •  4 orthologues, •  6 paralogues



[3] Orthologues

•  In this panel you can: 1- ‘jump’ to another species 2- see the protein pairwise alignment (2 way)


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[4] Paralogues

•  In this panel you can: 1- ‘jump’ to another species, 2- See the protein pairwise

alignment (2 way), 3- See the alignment of both

genomic regions (image)


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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

* Look in the Ensembl documentation��http://www.ensembl.org/info/docs/compara/index.html

vb tutorial-compara-update2010

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