Part I: Tips and Techniques from curators GBrowse at TAIR David Swarbreck.

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Part I: Tips and Techniques from curators GBrowse at TAIR David Swarbreck

TAIR9 Genome Release

TAIR9 - Sources of data New cDNA/EST data, x-species alignments Updates from proteome data Baerenfaller et al., 2008 and Castellana et al., 2008 Analysis of pseudopipe annotations Mark Gersteins lab Analysis of alternative gene predicitions Gnomon - Alexandre Souvorov Eugene - Sébastien Aubourg Aceview - Jean Thierry-Mieg

TAIR9 Genome release 282 new loci, 739 new gene models 1254 modified models, 774 CDS updates 1144 modified exons, 1056 new exons Contains: genes total, gene models 27,379 protein coding genes 4827 pseudogenes/TE genes 1312 ncRNAs

Genome Browsers at TAIR Two options (Seqviewer & GBrowse)

Seqviewer

GBrowse Header Main Browser Window Track Menu

GBrowse - Header Search by: Feature Name AT1G01040 AY Position Chr2: Configure Vista plot & fasta download

Track menu

Proteomics Data Baerenfaller 2008 Castellana et al. 2008

Reposition tracks

VISTA plot Gbrowse track Dubchak et al

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

Promoter Elements

Tracks updated regularly

Gene Confidence Rank Attributes confidence scores to all exons and gene models based on different types of experimental and computational evidence

Assigning A Confidence Rank E1 E4

Full support No support

How can I upload my own annotations to GBrowse ?

How can I download a marked up FASTA file of a particular region?

Decorated Fasta file

Coming Soon Synteny viewer