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Using WormBase to decipher parasitic nematode genomes

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  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