lecture_notes:05-17-2010
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lecture_notes:05-17-2010 [2010/05/17 21:47] hyjkim created |
lecture_notes:05-17-2010 [2010/06/01 18:39] (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=== | ||
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| + | 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. |
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| 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 21:47 by hyjkim
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