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lecture_notes:05-17-2010

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lecture_notes:05-17-2010 [2010/05/17 14:47]
hyjkim created
lecture_notes:05-17-2010 [2010/06/01 11:39] (current)
jlong Slides from presentation uploaded
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 ====Genome Annotation with RAST and Artemis==== ====Genome Annotation with RAST and Artemis====
 ===Presented by Jeff Long=== ===Presented by Jeff Long===
 +
 +Slides from presentation {{:​lecture_notes:​genomeannotation.pdf|genome annotation}}
  
 The RAST server: Rapid Annotations using Subsystems Technology The RAST server: Rapid Annotations using Subsystems Technology
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   - Takes some time to run: 1-2 weeks for a small genome (6-8mb).   - Takes some time to run: 1-2 weeks for a small genome (6-8mb).
   - The SEED Viewer is an annotation tool which gives you a pie chart for all the subsystems for all genes found.   - The SEED Viewer is an annotation tool which gives you a pie chart for all the subsystems for all genes found.
-  - Jeff showed a slide on Calothrix, a nitrogen fixing organism found in the ocean. +  - Jeff showed a slide on //Calothrix//, a nitrogen fixing organism found in the ocean. 
-    - Clicking on a subsystem would take you to a list of genes found within your organism.+    - Clicking on a subsystem ​(biosynthesis pathway) ​would take you to a list of genes found within your organism.
     - Genes found in the subsystem can be further evaluated in a detailed page.     - Genes found in the subsystem can be further evaluated in a detailed page.
-    - The data shown is very analgous to the UCSC genome browser.+    - The data format ​is analgous to the UCSC genome browser.
       - Shows you genes with similar DNA       - Shows you genes with similar DNA
  
-Assembly of the genome of Calothorix rhizosoleniae strain sc01, a marine nitrogen fixing cyanobacterium. +Assembly of the genome of //Calothorix rhizosoleniae// strain sc01, a marine nitrogen fixing cyanobacterium.
-  - +
  
 Nitrogen Fixation Nitrogen Fixation
-  - Take N2 gas and using it in organic ​nitrogen.+  - Take N2 gas and convert ​it into a bioavailabe form of nitrogen.
   - In the open ocean, there is a dearth of usable nitrogen.   - In the open ocean, there is a dearth of usable nitrogen.
-  - Calothorix has a string of heterocysts (nitrogen-fixing cells) and vegetative cells (oxygen utilizing cells)+  - //Calothorix// has a string of heterocysts (nitrogen-fixing cells) and vegetative cells (oxygen utilizing cells)
  
 Artemis Comparison tool (ACT) Artemis Comparison tool (ACT)
 +http://​www.sanger.ac.uk/​resources/​software/​artemis/​
   - Java-based programs that can be run from a browser.   - Java-based programs that can be run from a browser.
   - Artemis   - Artemis
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       - Shows information in embl format       - Shows information in embl format
   - DNA Plotter   - DNA Plotter
-    - Shows dna plaotted ​onto a circle-- Similar to circusGraphs ​program used by David Bernick.+    - Shows sequence plotted ​onto a circle-- Similar to CircOS ​program used by David Bernick.
   - WebACT   - WebACT
     - With closely related genomes, program draws the syntany between them.     - With closely related genomes, program draws the syntany between them.
lecture_notes/05-17-2010.1274132865.txt.gz · Last modified: 2010/05/17 14:47 by hyjkim