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lecture_notes:05-17-2010

Genome Annotation with RAST and Artemis

Presented by Jeff Long

Slides from presentation genome annotation

The RAST server: Rapid Annotations using Subsystems Technology

  1. Takes a genome and annotates them.
  2. When you enter the website, you can upload a genome and annotate it.
  3. Takes some time to run: 1-2 weeks for a small genome (6-8mb).
  4. The SEED Viewer is an annotation tool which gives you a pie chart for all the subsystems for all genes found.
  5. Jeff showed a slide on Calothrix, a nitrogen fixing organism found in the ocean.
    1. Clicking on a subsystem (biosynthesis pathway) would take you to a list of genes found within your organism.
    2. Genes found in the subsystem can be further evaluated in a detailed page.
    3. The data format is analgous to the UCSC genome browser.
      1. Shows you genes with similar DNA

Assembly of the genome of Calothorix rhizosoleniae strain sc01, a marine nitrogen fixing cyanobacterium.

Nitrogen Fixation

  1. Take N2 gas and convert it into a bioavailabe form of nitrogen.
  2. In the open ocean, there is a dearth of usable nitrogen.
  3. Calothorix has a string of heterocysts (nitrogen-fixing cells) and vegetative cells (oxygen utilizing cells)

Artemis Comparison tool (ACT) http://www.sanger.ac.uk/resources/software/artemis/

  1. Java-based programs that can be run from a browser.
  2. Artemis
    1. Overview window that is similar to the UCSC genome browser
    2. DNA view window shows the actual sequence.
    3. Feature table
      1. Shows information in embl format
  3. DNA Plotter
    1. Shows sequence plotted onto a circle– Similar to CircOS program used by David Bernick.
  4. WebACT
    1. With closely related genomes, program draws the syntany between them.
    2. Gives an instantaneous view of the similarity between two genomes.
    3. Maps which portions of genome map to another genome.
  5. BamView
    1. No details on this tool, but it comes packaged with ACT.
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lecture_notes/05-17-2010.txt · Last modified: 2010/06/01 11:39 by jlong