Artemis

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Artemis

• Michael Nuhn

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Artemis

• Display a genome with annotation
• Create and edit annotation

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Artemis GUI is divided into 3 sections
Display of the genome in two zoom levels
Short summary of the annotation
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Artemis
Genes
Stopcodons
On the highest zoomlevel translation into the 6
reading frames
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Artemis as a converter

• Artemis can save an annotated genome in different
  formats
• It can be used to convert from one format to the
  other.
• E.g. Genbank-gt EMBLor EMBL-gtfasta for Blast

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Artemis as a converter

• To convert a sequence to fasta formatWrite
  All Bases-gtFASTA Format

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The concept of entries

• The name of the file appears as an entry
• It is possible to load more than one entry.
• File-gtRead an entry
• The individual annotations are displayed as
  layers over the sequence.

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The concept of entries

• An annotation that is loaded in artemis appears
  as an entry.
• Additionally loaded entry
• Entries can be switched on or off

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The concept of entries

• Checkboxes determine which entries are shown
• They can be removed with Entries-gtRemove an
  Entry...

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The concept of entries

• Results from sequence analyses on the server can
  be loaded into Artemis as an entry.

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The concept of entries

• Searches for
• Motifs
• Promoters
• Loop structures

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The concept of entries

• Rho independent terminators

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The concept of entries

• ORFs with glimmer

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The concept of entries

• tRNAs

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• IS Elements

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The concept of entries

• Box Elements

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Back to Artemis

• Select features

Genes etc.
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Select features

• Artemis provides several options, to select
  features
• Click on feature with mouse
• Click on several features consecutively while
  holding the shift-button
• Use the Feature Selector under Select-gtFeature
  Selector

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Feature Selector

• Selections are possible by various criteria
• Example All genes where the gene name contains
  the name pbp

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Feature Selector

• By pushing the button View one obtains a list
  of the selected features

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Feature Selector

• One can go through the list one after another
• Artemis jumps to the corresponding location in
  the sequence