Genome Browser
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This document discusses GenomeBrowser. It mentions that the UCSC Human Genome Browser receives 50,000 hits per day and 3,000 users per day, while another receives 1,257 hits per day and 10 users per day. It also discusses various features of GenomeBrowser like being lightweight, configurable, and promoting data sharing.
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Genome Browser
- 1. GenomeBrowser GenomeBrowser Center for Genome Science, NIH, KCDC Hong ChangBum hongiiv@gmail.com
- 3. , Genome Browser 4 .
- 6. An Interview with Ewan Birney: Keynote Speaker at O’Relly’s Bioinformatics Technology Conference 2001/10
- 16. •UCSC Human Genome Browser •50,000 Hit/Day •3,000 users/Day • •1,257 Hit/Day •10 users/Day
- 17. Code Name : Acuvue Objective: !
- 21. 1 3 2
- 23. Google Maps API Presentation SNP Population Reference Link
- 25. •Part of Generic Model Organism Database Project •Lightweight & portable •Highly configurable •Clean user interface •Promotes data sharing
- 26. •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
- 27. •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.
- 29. •Add your own tracks •Add 3d party tracks •Distributed annotation system support
- 34. •Gbrowse on UCSC •Gbrowse on EnsEMBL •Gbrowse on both
- 37. •BioPerl and Bio::Graphics Software Libraries •Bio::DB::GFF Database •GadFly Database •Plug-ins
- 38. 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
- 39. !quot; !quot;#$ #$%&'%( )%&%
- 40. 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)
- 43. •“One Click” install on Macintosh OSX •“Three Click” install onWindows XP •“Tippity-tappity-tap” install on Linux/Solaris/BSD Unix
- 44. Genome Browser 10 % 90 %
- 45. 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;#$%&'(-(*+