Banana Slug Genomics

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====Genome Annotation with RAST and Artemis====
===Presented by Jeff Long===

The RAST server: Rapid Annotations using Subsystems Technology
  - Takes a genome and annotates them.
  - When you enter the website, you can upload a genome and annotate it.
  - 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.
  - 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.
    - Genes found in the subsystem can be further evaluated in a detailed page.
    - The data shown is very analgous to the UCSC genome browser.
      - Shows you genes with similar DNA

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

Nitrogen Fixation
  - Take N2 gas and using it in organic 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)

Artemis Comparison tool (ACT)
  - Java-based programs that can be run from a browser.
  - Artemis
    - Overview window that is similar to the UCSC genome browser
    - DNA view window shows the actual sequence.
    - Feature table
      - Shows information in embl format
  - DNA Plotter
    - Shows dna plaotted onto a circle-- Similar to circusGraphs program used by David Bernick.
  - WebACT
    - With closely related genomes, program draws the syntany between them.
    - Gives an instantaneous view of the similarity between two genomes.
    - Maps which portions of genome map to another genome.
  - BamView
    - No details on this tool, but it comes packaged with ACT.
Banana Slug Genomics

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