SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI,...
-
Upload
timothy-griffin -
Category
Documents
-
view
217 -
download
0
Transcript of SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI,...
![Page 1: SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022062320/56649f585503460f94c7de9f/html5/thumbnails/1.jpg)
SRI International Bioinformatics1
Genome Browser
Tomer Altman
Bioinformatics Research Group
SRI, International
August 19th, 2009
![Page 2: SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022062320/56649f585503460f94c7de9f/html5/thumbnails/2.jpg)
SRI International Bioinformatics2
Navigator Genome Browser
The Pathway Tools Navigator allows you to browse the replicons (chromosomes or plasmids) of your PGDB.
Can be accessed a few different ways: Click on the replicon or Transcription Units listed on a single
organism display Click on the base pair coordinates of a gene display Menu: Chromosome --> Select & Browse Chromosome/Replicon
![Page 3: SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022062320/56649f585503460f94c7de9f/html5/thumbnails/3.jpg)
SRI International Bioinformatics3
From Current Organism:
![Page 4: SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022062320/56649f585503460f94c7de9f/html5/thumbnails/4.jpg)
SRI International Bioinformatics4
From Gene Display:
![Page 5: SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022062320/56649f585503460f94c7de9f/html5/thumbnails/5.jpg)
SRI International Bioinformatics5
From Menu:
![Page 6: SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022062320/56649f585503460f94c7de9f/html5/thumbnails/6.jpg)
SRI International Bioinformatics6
The Genome Browser
![Page 7: SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022062320/56649f585503460f94c7de9f/html5/thumbnails/7.jpg)
SRI International Bioinformatics7
Browser Navigation
The full-length, low-resolution chromosome map is shown at the top, with the selected region in red.
A few lines from the selected region are shown below, in higher resolution.
Magnification: Click on the top, low-resolution chromosome map Specifying the start & end base-pair positions Entering a gene name Navigation arrows
![Page 8: SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022062320/56649f585503460f94c7de9f/html5/thumbnails/8.jpg)
SRI International Bioinformatics8
Navigation Features
![Page 9: SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022062320/56649f585503460f94c7de9f/html5/thumbnails/9.jpg)
SRI International Bioinformatics9
Browser Diagram
Gene blocks with arrows pointing from 5' to 3'ORFs for proteins have symmetrical arrowheadsRNA genes have asymmetrical arrowheadsPhantom or pseudo-genes are crossed outGenes wrapping around line have 'zig-zag'Genes assigned to transcription unit (TU) are coloredGrey boxes in background also signify TU membershipPromoters and terminators are also displayed
![Page 10: SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022062320/56649f585503460f94c7de9f/html5/thumbnails/10.jpg)
SRI International Bioinformatics10
Browser Legend
![Page 11: SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022062320/56649f585503460f94c7de9f/html5/thumbnails/11.jpg)
SRI International Bioinformatics11
Chromosome Menu
Select & Browse Chromosome/Replicon For PGDBs with multiple replicons
Show Sequence of a Segment of Chromosome Sub-sequence of the replicon, or its reverse-compliment
Print Poster Generate a wall poster-sized PostScript file with the entire genome
displayedAdd External Track
Display GFF file data in context
![Page 12: SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022062320/56649f585503460f94c7de9f/html5/thumbnails/12.jpg)
SRI International Bioinformatics12
Displaying External Tracks on the Genome Browser
External tracks can be displayed on a chromosome region using the GFF, version 2, file format
Flexible format can display various kinds of data: alternate gene predictions, gene expression data, etc.
Each feature line has a start and end position, and optionally a numeric score value.
![Page 13: SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022062320/56649f585503460f94c7de9f/html5/thumbnails/13.jpg)
SRI International Bioinformatics13
How to Display External Tracks:
Menu: Chromosome -> Select & Browse Chromosome/Replicon
Click “Show Tracks”Menu: Chromosome -> Add External TrackEnter URL or browse local filesCan be repeated multiple times to display several data
sets
![Page 14: SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022062320/56649f585503460f94c7de9f/html5/thumbnails/14.jpg)
SRI International Bioinformatics14
Browser with Tracks Shown
![Page 15: SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022062320/56649f585503460f94c7de9f/html5/thumbnails/15.jpg)
SRI International Bioinformatics15
The Genome Overview Omics Viewer
The maximum zoom-out level for the Genome Browser is also known as the Genome Overview
You can use the Genome Overview to get a snapshot of the overall gene content for a given replicon
It can also be used to display high-throughput biological experiment data as one of Pathway Tools' Omics Viewers
![Page 16: SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022062320/56649f585503460f94c7de9f/html5/thumbnails/16.jpg)
SRI International Bioinformatics16
Genome Omics Viewer
![Page 17: SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022062320/56649f585503460f94c7de9f/html5/thumbnails/17.jpg)
SRI International Bioinformatics17
Comparative Genome Browser
To enter, in Gene page, click on “Align in Multi-Genome Browser”
“Select Allowed Organisms” for what to compare toComparison only works when Ortholog-Links are
presentThe selected gene is centered, and aligned with
Orthologs in the other PGDBsColors mean shared Orthologs. A dozen colors are
reused.
![Page 18: SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022062320/56649f585503460f94c7de9f/html5/thumbnails/18.jpg)
SRI International Bioinformatics18
Comparative Genome Browser Display
![Page 19: SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022062320/56649f585503460f94c7de9f/html5/thumbnails/19.jpg)
SRI International Bioinformatics19
Ortholog-Links
Can be stored as DBLINKS on gene frameshttp://bioinformatics.ai.sri.com/ptools/ortholog-link-
setup.htmlProblem when many PGDBs: grows as N2
Ortholog-Link MySQL DB is used for BioCyc WWW siteContact [email protected] for setup