Genome Browser

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UCSC, NCBI MapView, Ensembl, Gbrowse

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Genome Browser

  1. 1. GenomeBrowser GenomeBrowser Center for Genome Science, NIH, KCDC Hong ChangBum hongiiv@gmail.com
  2. 2. 
 

  3. 3. , Genome Browser 4 .
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  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
  22. 22. 
 •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
  24. 24. 
 •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
  30. 30. 
 •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
  32. 32. 
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  33. 33. 
 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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  36. 36. •“One Click” install on Macintosh OSX •“Three Click” install onWindows XP •“Tippity-tappity-tap” install on Linux/Solaris/BSD Unix
  37. 37. Genome Browser 10 % 90 %
  38. 38. 4.*(#/,'(5 Hong ChangBum Center for Genome Science NIH, KCDC !quot;0*$1,.23quot;' hongiiv@gmail.com !quot;#quot;$%"'()*&$+,-.#/,'( !quot;#$%&'()*!'+,-.#& http://socmaster.homelinux.org/~hongiiv /++0122quot;3#4-!'5*quot;#$%&'(-(*+

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