1 / 26

Using WormBase to decipher parasitic nematode genomes

Using WormBase to decipher parasitic nematode genomes. Caenorhabditis elegans. WormBase = 30 people, ~4 centers. Sanger and EBI / Cambridge: Matt Berriman Paul Kersey Gary Williams Mary Ann Tuli Paul Davis Ed Griffiths Washington University / St. Louis: John Spieth Tamberlyn Bieri

olina
Download Presentation

Using WormBase to decipher parasitic nematode genomes

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Using WormBase to decipher parasitic nematode genomes ICOPA XII, August 2010

  2. Caenorhabditis elegans

  3. WormBase = 30 people, ~4 centers Sanger and EBI / Cambridge: Matt Berriman Paul Kersey Gary Williams Mary Ann Tuli Paul Davis Ed Griffiths Washington University / St. Louis: John Spieth Tamberlyn Bieri Phil Ozersky Bill Nash OICR / Vancouver: Lincoln Stein Todd Harris Nori de la Cruz Abigail Cabunoc Xiaoqi Shi CalTech / Pasadena: Paul Sternberg Kimberley Van Auken Karen Yook Cecilia Nakamura Juancarlos Chan Ruihua Fang Chris Grove Raymond Lee Wen Chen Jolene Fernandez Xiaodong Wang Ranjana Kishore Daniel Wang Gary Schindelman Hans-Michael Müller CSHL: Lincoln Stein

  4. WormBase -- one Web site, many roles

  5. From WormBase to WormsBase Tier I: C. elegans C. briggsae C. remanei Tier II: Caenorhabditis, Pristionchus, some pathogens Elegans C. brenneri C. elegans Caenorhabditis Tier III: others C. japonica C. sp 3 PS1010 Droso-philae C. drosophilae C. sp. 1 SB341 Heterorhabditis bacteriophora Haemonchus contortus Pristionchus pacificus Meloidogyne hapla Meloidogyne incognita Brugia malayi

  6. Near-future genome additions Heterorhabditis bacteriophora (WashU): insect parasite Pristionchus pacificus (Max Planck): associated with beetles Strongyloides ratti (Sanger): rat parasite Ascaris suum (Sanger): pig parasite; proteomics Brugia malayi (WashU): human lymphatic filariasis Onchocerca volvulus (Sanger): human river blindness Trichinella spiralis (WashU/Sanger): human trichinellosis

  7. Genomic synteny: 3 Caenorhabditis spp.

  8. Gene orthology: Y50D4A.2/WRB ICOPA, August 2010

  9. Homologous protein domains: MLT-10

  10. "Generic My/Many Organism" software www.gmod.org

  11. Multiple, colinear views of a genome

  12. Textpresso: full-text literature searches www.textpresso.org

  13. WormMart: user-specified data searches

  14. WormBook: free Web encyclopedia www.wormbook.org Editors: M. Chalfie and J. Mendel

  15. Reactome: conserved pathways

  16. WormAtlas: cell types in detail

  17. Wiki: an instantly editable user's guide

  18. Getting data in bulk #!/usr/bin/env perl use Ace; # AcePerl.pm: interface with ACeDB databaseuse strict; my $db = Ace->connect(-host=>'mining.wormbase.org', port=>'2005') or die "Can't connect to the server: $!"; # List all of the genes in the Unc gene_classmy $gene_class = $db->fetch(Gene_class=>'unc');my @genes = $gene_class->Genes;foreach my $gene (@genes) { print join("\t", $gene, $gene->Public_name),"\n";} # Use port 3306 for MySQL queries via Bio:DB::GFF # or Bio::DB::SeqFeature mining.wormbase.org

  19. Gene pages act as data hubs

  20. Human-readable gene descriptions

  21. Expression patterns with defined reagents http://wormbase.org/db/gene/expression? name=Expr2929;class=Expr_pattern Ikegami et al. (2004), Dev. Cell. 6, 383-395.

  22. Phenotype ontology Hierarchy-based ontology 1849 terms 100% defined 73% associated with an annotation

  23. Navigating WormBase help@wormbase.org

  24. WormBase ambitions / summary 1. In support of any species, provide coherent online environment. http://wormbase.org/YOUR_SPECIES http://wormbase.org/YOUR_SPECIES/blog http://wormbase.org/YOUR_SPECIES/wiki http://wormbase.org/YOUR_SPECIES/data 2. Provide each community basic similarity searching. http://wormbase.org/YOUR_SPECIES/blast 3. Provide foundational browsing (genome, gene pages). 4. Provide easy linkage to relevant C. elegans biology.

  25. Acknowledgements: • WormBase Consortium • NIH/NHGRI • C. elegans research community

More Related