Codon Table Library

The Codon Table Library is part of the Library Explorer, where codon tables can be stored for use in backtranslation or sequence viewing.

Organization

  • Codon tables are organized within folders.
    • The toolbox is pre-loaded with a set of codon tables.
  • New folders can be created by selecting “add new folder / group” from the “add” button at the bottom of the Library Explorer.
  • A folder may be moved within the codon table library by selecting the icon and dragging it to a new position.

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Adding, removing and editing codon tables

  • A table may be added to the toolbox by
    • selecting “add new codon table” from the “add” button at the bottom of the Library Explorer.
    • copying an existing table in the library (not yet working in the beta version)
      • by right clicking on the icon and selecting “copy codon table”
      • by dragging the icon of the table to a new position in the library while holding down the ctrl key
  • A table may be deleted from the library by selecting it and clicking on the “delete” button at the bottom of the Library Explorer.
  • A table may be edited within the toolbox by
    • selecting it and clicking on the “edit” button at the bottom of the Library Explorer.
    • double clicking on it.

Importing codon tables using DNA2.0's web service

  • A table may be imported into the toolbox by
    • selecting “import codon table” from the “add” button at the bottom of the Library Explorer (not yet working in the beta version).
    • selecting “import codon table” from the “File” menu in the Construct Editor

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  • The desired table can be located by typing in part of the name of the organism into the search window
    • the search works using genus / species names
    • common names can also be useful
      • try searching for “human” to get a sense of the search process

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Codon table format

  • Codon tables contain frequency data:
    • The “codon count” column is the only one that can be edited; it represents the number of times that each codon occurs within the genes of the selected organism.
    • All of the other columns are calculated from the count data.
  • Tables can be sorted by codon or amino acid by clicking on the column header.

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Preloaded tables are different

  • Preloaded tables may be updated from time to time with new versions of GeneDesigner. They therefore differ from user-added tables in the following ways:
Moving pre-loaded tables
  • Moving a pre-loaded table will automatically create a copy of the table.
    • When tables are updated, only the tables in their original locations will be updated.
Editing pre-loaded tables
  • Pre-loaded tables must be copied before editing.
Deleting pre-loaded tables
  • Pre-loaded tables cannot be deleted.
 
ui/codon_table_library.txt · Last modified: 2018/01/17 08:09 (external edit)
 
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