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TAIR, PMN, SGN and Gramene workshop

TAIR, PMN, SGN and Gramene workshop. Focus on comparative genomics and new tools. Philippe Lamesch, A. S. Karthikeyan, Aureliano Bombarely Gomez, Pankaj Jaiswal. TAIR. Genome Browsers Synteny Viewer Protein interaction Viewer. Tools at TAIR. Genome Browsers at TAIR.

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TAIR, PMN, SGN and Gramene workshop

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  1. TAIR, PMN, SGN and Gramene workshop Focus on comparative genomics and new tools Philippe Lamesch, A. S. Karthikeyan, Aureliano Bombarely Gomez, Pankaj Jaiswal

  2. TAIR • Genome Browsers • Synteny Viewer • Protein interaction Viewer

  3. Tools at TAIR

  4. Genome Browsers at TAIR • Two options (Seqviewer & GBrowse)

  5. Seqviewer

  6. Seqviewer

  7. GBrowse Header Main Browser Window Track Menu

  8. GBrowse - Header Search by: Feature Name AT1G01040 AY438620 Position Chr2:100500..102500 Configure Vista plot & fasta download

  9. Track menu

  10. Proteomics Data • Baerenfaller 2008 • Castellana et al. 2008

  11. Reposition tracks

  12. Promoter Elements Yamamoto YY, Obokata J. (2008) Nucleic Acids Res 36, D977-D981

  13. Tracks updated regularly

  14. Full support No support

  15. VISTA plot Gbrowse track Dubchak et al

  16. Nucleotide conservation across large evolutionary time spans Arabidopsis Populus (92 Mya) Medicago (92 Mya) Oryza (160 Mya) Selaginella (400 Mya) Physcomitrella (450 Mya) TAIR GBrowse: http://arabidopsis.org/cgi-bin/gbrowse/arabidopsis/

  17. Nucleotide conservation across large evolutionary time spans Arabidopsis Phot1 blue light photoreceptor Populus (92 Mya) Medicago (92 Mya) Oryza (160 Mya) Selaginella (400 Mya) Physcomitrella (450 Mya) TAIR GBrowse: http://arabidopsis.org/cgi-bin/gbrowse/arabidopsis/

  18. LBL: http://pipeline.lbl.gov/cgi-bin/textBrowser2?act=hits&run=74-&base=174&pos=chr3:16826523-16836522

  19. Orthologs and Gene Families INSECTS Aedes aegypti (Yellow fever mosquito) Anopheles gambiae (Malaria mosquito) Apis mellifera (Western honeybee) Drosophila melanogster (Fly) Drosophila pseudoobscura (Fly) MAMMALS Bos taurus (Cow) Canis familiaris (Dog) Homo sapiens (human) Mus Musculus (mouse) Gallus gallus (Chicken) Macaca mulatta (Rhesus Macaque) Monodelphis domestica (Opossum) Pan troglodytes (Chimpanzee) Rattus norvegicus (Rat) YEAST Candida gablata (Haploid yeast) Cryptococcus neoformans (Yeast-like fungus) Debaryomyces hansenii (Yeast) Kluyveromyces lactis (Yeast) Yarrowia lipolytica (yeast) Schizosaccharomyces pombe (Fission yeast) Saccharomyces cerevisiae (Budding yeast) FISH Takifugu rubripes (Pufferfish/Fugu) Tetraodon nigroviridis (Pufferfish/Green-spotted) Gasterosteus aculeatus (Stickleback) Danio rerio (Zebrafish) NEMATODES Caenorhabditis elegans (Nematode) Caenorhabditis briggsae (Nematode) Caenorhabditis remanei (Nematode) PLANTS Oryza sative (rice) OTHER Xenopus tropicalis (Frog) Ciona intestinalis (Sea squirt) Entamoeba histolytica (Amoebozoa) Dictyostelium discoideum (Slime mold)

  20. Orthologs and Gene Families

  21. Other ways to navigate between genomes: Brassica and radish sequences Brassica - 840,000 ESTs, 2100 cDNAs Raphanus - 287,000 ESTs Nucleotide alignments to Arabidopsis using CAT (Cross-species Alignment Tool, Li et al 2007) TAIR GBrowse

  22. TAIR survey April 2008

  23. TAIR survey April 2008 What tools should we add to TAIR?

  24. TAIR survey April 2008 What tools should we add to TAIR? Synteny Viewer Protein-Protein Interaction Viewer

  25. Synteny Viewer • GBrowse_syn: GBrowse-based synteny browser developed by Sheldon McKay • Helps to study and analyze syntenic regions, homologous genes and other conserved elements between sequences • By comparing less studied genomes to the well annotated Arabidopsis genome in Gbrowse_syn, scientists can identify novel genes and putative regulatory elements. • First version of TAIR synteny viewer contains A.thaliana to A. lyrata genome alignments (more will be added soon)

  26. Synteny Viewer

  27. Synteny Viewer

  28. TAIR Protein-Protein interaction viewer using N-browse • Protein-protein interactions curated by Intact, Biogrid and TAIR • Using the generic network browser N-browse developed by the Gunsalus Lab (Curr Protoc Bioinformatics. 2008 Sep; Chapter 9:Unit 9.11) • First version contains interactions determined experimentally • Interactions can be filtered by type of experiment and biological modules • User can overlay own interaction set on curated set

  29. Minimal information about an Interaction http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI

  30. Arabidopsis Protein-Protein interaction viewer > 1,500 interactions in TAIR Nbrowse Interaction Viewer

  31. Acknowledgments TAIR Tech Team: Vanessa Kirkuo Chris Wilks Tom Meyer Cindy Lee Raymond Chetty Bob Muller PIs Eva Huala Sue Rhee Curators David Swarbreck Donghui Li Tanya Berardini Kate Dreher Peifen Zhang N-Browse Kris Gunsalus (NYU) Mark Gibson Gbrowse_syn Sheldon McKay (CSHL) Vista Browser Ina Dubchak (LBNL)

  32. Other ways to navigate between genomes: Orthologs and gene families TAIR GBrowse: http://arabidopsis.org/cgi-bin/gbrowse/arabidopsis/

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