GenomeBrowser
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Transcript of GenomeBrowser
![Page 1: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/1.jpg)
GenomeBrowser
![Page 2: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/2.jpg)
우리는 그들을 홍콩의4대천황으로 기억합니다.
![Page 3: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/3.jpg)
잘 보세요, 이제부터
Genome Browser4대 천황을 소개합니다.
![Page 4: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/4.jpg)
그럼, GenomeBrowser는 무엇인가요?
![Page 5: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/5.jpg)
![Page 6: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/6.jpg)
분자생물학자들에게 그들이 웹 에서 인간과 쥐의 유전체에 대해 질문할 수 있는
첫번째 장소가 되기를 바랍니다. 분자생물학자들이 엉망진창인 데이터를 추적하느라 아까
운 시간을 소비하지 않고 그들에게 흥미로운 것들을 신속히 발견하고 그래서 실제적인 실험을 계획하고 진행할 수 있도록 훌륭한 웹사이트에서 시간을 보낼 수 있
기를 바랍니다.
Ensembl 인간 유전체 서버 프로젝트는 무엇인지 자세히 설명 부탁드립니다.
An Interview with Ewan Birney: Keynote Speaker at O’Relly’s Bioinformatics Technology Conference 2001/10
![Page 7: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/7.jpg)
UCSCGenomeBrowser
![Page 8: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/8.jpg)
EnsEMBL
![Page 9: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/9.jpg)
NCBIMapViewser
![Page 10: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/10.jpg)
GBrowse
![Page 11: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/11.jpg)
![Page 12: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/12.jpg)
Oops!!!!
잠깐실망하고
갑시다.
![Page 13: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/13.jpg)
![Page 14: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/14.jpg)
KSNPDBBrowser
![Page 15: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/15.jpg)
kGeneDBBrowser
![Page 16: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/16.jpg)
LesVisiteurs
•UCSC Human Genome Browser•50,000 Hit/Day
•3,000 users/Day
•보건의료유전체사업정보
•1,257 Hit/Day•10 users/Day
![Page 17: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/17.jpg)
Code Name : AcuvueObjective: 하루만에 끝내버리자!
![Page 18: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/18.jpg)
KAREData(3.07GB)
![Page 19: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/19.jpg)
9,604Rows
500,000Cols
![Page 20: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/20.jpg)
KAREDataBaseScheme
![Page 21: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/21.jpg)
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DataBaseTables
![Page 22: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/22.jpg)
KAREBrowser
![Page 23: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/23.jpg)
Google Maps API 기반의 이미지 데이터 Presentation
외부 Reference LinkSNP Population 정보
![Page 24: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/24.jpg)
JustRight-LincolnStein
![Page 25: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/25.jpg)
GMODGbrowse
•Part of Generic Model Organism Database Project•Lightweight & portable•Highly configurable•Clean user interface•Promotes data sharing
![Page 26: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/26.jpg)
BrowsingaRegionoftheGenome
•Find your Favorite Gene•Find your Favorite Domain•Find your Favorite Oligo•Zoom - Low Magnification•Zoom - Medium Magnification•Zoom - High Magnification•Zoom - Highest Magnification•Custom Tracks
![Page 27: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/27.jpg)
ExtensivelyCustomizable
•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.
![Page 28: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/28.jpg)
ExtensivelyExtensible
DAS Adaptor
Remote Source
Glyphs
![Page 29: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/29.jpg)
DataSharing
•Add your own tracks•Add 3d party tracks•Distributed annotation system support
![Page 30: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/30.jpg)
AddingyourOwnTracks
![Page 31: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/31.jpg)
Internationalization
![Page 32: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/32.jpg)
Adding3dPartyTracks
![Page 33: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/33.jpg)
GbrowseonRemoteSources
DAS Adaptor
UCSC Genome Browser
Glyphs
![Page 34: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/34.jpg)
DAS•Gbrowse on UCSC•Gbrowse on EnsEMBL•Gbrowse on both
![Page 35: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/35.jpg)
![Page 36: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/36.jpg)
DistributedGBrowse
Gbrowse 1
Gbrowse 2
Gbrowse 3
My Gbrowse
![Page 37: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/37.jpg)
GbrowseInternals
•BioPerl and Bio::Graphics Software Libraries•Bio::DB::GFF Database•GadFly Database •Plug-ins
![Page 38: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/38.jpg)
GFF3andBio::DB::GFFDatabaseseqid source type start end score strand phase attributeChr1 dbsnp snp 200 300 . + . ID=SNP:rs1234;alleles:G/TChr1 dbsnp snp 400 700 . + . ID=SNP:rs4321;alleles:G/T
![Page 39: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/39.jpg)
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)
BinningScheme(R-Tree)
![Page 40: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/40.jpg)
>400-foldfaster
![Page 41: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/41.jpg)
ConfiguringGbrowse
![Page 42: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/42.jpg)
Installation
•“One Click” install on Macintosh OSX•“Three Click” install on Windows XP•“Tippity-tappity-tap” install on Linux/Solaris/BSD Unix
![Page 43: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/43.jpg)
10 %
데이터
충분한 대역폭
협력체계 구축
하드웨어
외적 요소
훌륭한 Genome Browser의 조건
내적 요소
이미지
연구 개발을 위한 개방된 인프라스트럭처
서비스 안정성
대용량 데이터 처리
코드의 재사용성
알고리즘
데이터베이스 디자인
90 %
사용성
![Page 44: GenomeBrowser](https://reader033.fdocuments.in/reader033/viewer/2022052905/5584f0b1d8b42a30708b4c28/html5/thumbnails/44.jpg)
QnA