GenomeBrowser
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The document discusses Genome Browser, a lightweight and portable genome browsing software. It can be configured and customized easily. It promotes data sharing through tracks and supports the Distributed Annotation System (DAS) for adding third-party data. The software uses common bioinformatics libraries and has easy installation methods for various operating systems.
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GenomeBrowser
- 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. 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)
- 42. •“One Click” install on Macintosh OSX •“Three Click” install onWindows XP •“Tippity-tappity-tap” install on Linux/Solaris/BSD Unix
- 43. Genome Browser 10 % 90 %