GenomeBrowser

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General Genome Browser

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GenomeBrowser

  1. 1. GenomeBrowser
  2. 2. 
 

  3. 3. , Genome Browser 4 .
  4. 4.
  5. 5. An Interview with Ewan Birney: Keynote Speaker at O’Relly’s Bioinformatics Technology Conference 2001/10
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  11. 11. 
 •UCSC Human Genome Browser •50,000 Hit/Day •3,000 users/Day • •1,257 Hit/Day •10 users/Day
  12. 12. Code Name : Acuvue Objective: !
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  16. 16. 1 3 2 

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  18. 18. Google Maps API Presentation SNP Population Reference Link
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  20. 20. 
 •Part of Generic Model Organism Database Project •Lightweight & portable •Highly configurable •Clean user interface •Promotes data sharing
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 •Find your Favorite Gene •Find your Favorite Domain •Find your Favorite Oligo •Zoom - Low Magnification •Zoom - Medium Magnification •Zoom - High Magnification •Zoom - Highest Magnification •CustomTracks
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 •End-user •Turn tracks on and off, change order, change packing & labeling attributes(stored in cookie) •Data provider •Change fonts, colors, text. •Change overview-genetic map, contigs, coverage, karyotype. •Define new tracks using simple config file. •Tinker with track appearance to hearts content.
  23. 23. 
 Glyphs DAS Adaptor Remote Source
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 •Add your own tracks •Add 3d party tracks •Distributed annotation system support
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 Glyphs DAS Adaptor UCSC Genome Browser
  28. 28. •Gbrowse on UCSC •Gbrowse on EnsEMBL •Gbrowse on both
  29. 29. 
 Gbrowse 2 Gbrowse 1 Gbrowse 3 My Gbrowse
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 •BioPerl and Bio::Graphics Software Libraries •Bio::DB::GFF Database •GadFly Database •Plug-ins
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 seqid source type start end score strand phase attribute Chr1 dbsnp snp 200 300 . + . ID=SNP:rs1234;alleles:G/T Chr1 dbsnp snp 400 700 . + . ID=SNP:rs4321;alleles:G/T
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 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 A B C (1,2,3,7,8,9,10,11) (1,4,14,15,16,17) (1,5,20)
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  35. 35. •“One Click” install on Macintosh OSX •“Three Click” install onWindows XP •“Tippity-tappity-tap” install on Linux/Solaris/BSD Unix
  36. 36. Genome Browser 10 % 90 %
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