GBrowse at TAIR Philippe Lamesch TAIR curator. Seqviewer.

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Presentation transcript:

GBrowse at TAIR Philippe Lamesch TAIR curator

Seqviewer

GBrowse Header Main Browser Window Track Menu

Track menu

TAIR GBrowse tracks Gene DNA Community annotations Sequence similarity Assembly Proteomics Analysis Expression Orthologs & Gene Families Variation Genomic Features Methylation

TAIR GBrowse tracks Gene DNA Community annotations Sequence similarity Assembly Proteomics Analysis Expression Orthologs & Gene Families Variation Genomic Features Methylation

Genes

Transposon element genes

TAIR GBrowse tracks Gene DNA Community annotations Sequence similarity Assembly Proteomics Analysis Expression Orthologs & Gene Families Variation Genomic Features Methylation

Alternative gene annotations Eugene (transcript, proteins +) Sebastien Aubourg Gnomon (transcript, proteins) Souvorov (NCBI) Aceview (transcript) Thierry-Mieg (NCBI) Hanada et al 2007 (3633 predicted genes)

TAIR GBrowse tracks Gene DNA Community annotations Sequence similarity Assembly Proteomics Analysis Expression Orthologs & Gene Families Variation Genomic Features Methylation

Assembly updates - GBrowse Gaps

TAIR GBrowse tracks Gene DNA Community annotations Sequence similarity Assembly Proteomics Analysis Expression Orthologs & Gene Families Variation Genomic Features Methylation

Proteomics Data High-density Arabidopsis proteome map (Baerenfaller. 2008)

Proteomics Data

TAIR GBrowse tracks Gene DNA Community annotations Sequence similarity Assembly Proteomics Analysis (Comparative) Expression Orthologs & Gene Families Variation Genomic Features Methylation

VISTA plot Gbrowse track Dubchak et al

TAIR GBrowse tracks Gene DNA Community annotations Sequence similarity Assembly Proteomics Analysis (Comparative) Expression Orthologs & Gene Families Variation Genomic Features Methylation

Transcriptome data

TAIR GBrowse tracks Gene DNA Community annotations Sequence similarity Assembly Proteomics Analysis (Comparative) Expression Orthologs & Gene Families Variation Genomic Features Methylation

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)

Orthologs and Gene Families

TAIR GBrowse tracks Gene DNA Community annotations Sequence similarity Assembly Proteomics Analysis (Comparative) Expression Orthologs & Gene Families Variation Genomic Features Methylation

Variation

TAIR GBrowse tracks Gene DNA Community annotations Sequence similarity Assembly Proteomics Analysis (Comparative) Expression Orthologs & Gene Families Variation Genomic Features Methylation

Promoter Elements

TAIR GBrowse tracks Gene DNA Community annotations Sequence similarity Assembly Proteomics Analysis (Comparative) Expression Orthologs & Gene Families Variation Genomic Features Methylation

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