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GenomeBrowser
1.
GenomeBrowser
2.
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, Genome Browser 4
.
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An Interview with
Ewan Birney: Keynote Speaker at O’Relly’s Bioinformatics Technology Conference 2001/10
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•UCSC Human Genome
Browser •50,000 Hit/Day •3,000 users/Day • •1,257 Hit/Day •10 users/Day
17.
Code Name :
Acuvue Objective: !
18.
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20.
21.
1
3 2
22.
23.
Google Maps API
Presentation SNP Population Reference Link
24.
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.
28.
Glyphs DAS Adaptor Remote Source
29.
•Add your own
tracks •Add 3d party tracks •Distributed annotation system support
30.
31.
32.
33.
Glyphs DAS Adaptor UCSC Genome Browser
34.
•Gbrowse on UCSC •Gbrowse
on EnsEMBL •Gbrowse on both
35.
36.
Gbrowse 2 Gbrowse 1 Gbrowse 3 My Gbrowse
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)
40.
41.
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•“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 %
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