part i: tips and techniques from curators gbrowse at tair david swarbreck
TRANSCRIPT
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Part I: Tips and Techniques from curators
GBrowse at TAIR
David Swarbreck
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TAIR9 Genome Release
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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 Gerstein’s lab
• Analysis of alternative gene predicitions• Gnomon - Alexandre Souvorov• Eugene - Sébastien Aubourg • Aceview - Jean Thierry-Mieg
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TAIR9 Genome release
• 282 new loci, 739 new gene models• 1254 modified models, 774 CDS updates• 1144 modified exons, 1056 new exons
• Contains: 33518 genes total, 39640 gene models
• 27,379 protein coding genes• 4827 pseudogenes/TE genes• 1312 ncRNAs
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Genome Browsers at TAIR
• Two options (Seqviewer & GBrowse)
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Seqviewer
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Seqviewer
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GBrowseHeader
Main Browser Window
Track Menu
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GBrowse - Header
Search by:
Feature Name AT1G01040
AY438620
Position Chr2:100500..102500
Configure Vista plot & fasta download
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Track menu
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Proteomics Data•Baerenfaller 2008
•Castellana et al. 2008
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Reposition tracks
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VISTA plot Gbrowse track
Dubchak et al
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Orthologs and Gene Families
INSECTSAedes aegypti (Yellow fever mosquito)Anopheles gambiae (Malaria mosquito)
Apis mellifera (Western honeybee)Drosophila melanogster (Fly)
Drosophila pseudoobscura (Fly)
MAMMALSBos 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)
YEASTCandida 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)
FISHTakifugu rubripes (Pufferfish/Fugu)
Tetraodon nigroviridis (Pufferfish/Green-spotted)Gasterosteus aculeatus (Stickleback)
Danio rerio (Zebrafish)
NEMATODESCaenorhabditis elegans (Nematode)Caenorhabditis briggsae (Nematode)Caenorhabditis remanei (Nematode)
PLANTSOryza sative (rice)
OTHERXenopus tropicalis (Frog)
Ciona intestinalis (Sea squirt)Entamoeba histolytica (Amoebozoa)
Dictyostelium discoideum (Slime mold)
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Orthologs and Gene Families
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Promoter Elements
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Tracks updated regularly
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Gene Confidence Rank
• Attributes confidence scores to all exons and gene models based on different types of experimental and computational evidence
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Assigning A Confidence Rank
E1
E4
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Full support
No support
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How can I upload my own annotations to GBrowse ?
http://www.arabidopsis.org/cgi-bin/gbrowse/arabidopsis/?help=annotation
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How can I download a marked up FASTA file of a particular region?
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Decorated Fasta file
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Decorated Fasta file
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Coming Soon Synteny viewer