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Calculate codon usage

Codon usage tables can be calculated and written to the Output Window, and written to disk. If required the values found can be added to the counts in a pre-existing codon table, or when written out to disk they can be concatenated with an existing codon table file. In the first case the existing file will be read and added to the values calculated for the region defined by the user. In the latter, the values calculated for the region defined by the user will be written immediately after those from the existing table, hence producing a pair of tables joined end to end. An example of this is shown at the end of this section, and a more typical result is shown below.

(Click for full size image)

Refering to the figure of the dialogue below, the user can select the range and strand over which to count. Note that irrespective of the strand being counted, the positions in the sequence are always defined from the current 5' end. i.e. to count over bases 1 to 100 the user should set the Start position to 1 and the End position to 100. The values in the table can be expressed as observed counts or as percentages of usage for the cognate amino acid.


The table can be output as a single table (as shown above), or as a double table (shown below). The user can request that the counts from an existing table be read and added to the counts which are about to be calculated, in which case the "File name" text window will be activated. If the user selects to output a double table, this dialogue will also be activated. To save the output in the selected form to a file, the user should fill in the "Save table to" text window.

Two of the protein coding search functions ( see section Codon usage method) and ( see section Author test) work best using a double codon table. The top table should contain the codon usage for the coding regions and the bottom table the usage for non-coding regions. A typical double codon table of this sort is shown below.

      F ttt     4 S tct    30 Y tat     5 C tgt     9
      F ttc    35 S tcc    21 Y tac    15 C tgc     5
      L tta     4 S tca     7 * taa     0 * tga     0
      L ttg    24 S tcg     9 * tag     0 W tgg    15
      L ctt    71 P cct     1 H cat    17 R cgt    37
      L ctc    39 P ccc     2 H cac    15 R cgc    18
      L cta     0 P cca    14 Q caa    87 R cga     1
      L ctg     4 P ccg     0 Q cag    18 R cgg     1
      I att    33 T act    30 N aat    12 S agt     2
      I atc    53 T acc    20 N aac    59 S agc     5
      I ata     1 T aca     3 K aaa    23 R aga    38
      M atg    32 T acg     0 K aag   117 R agg     0
      V gtt    30 A gct    71 D gat    58 G ggt     5
      V gtc    22 A gcc    54 D gac    32 G ggc     1
      V gta     7 A gca     6 E gaa    76 G gga    49
      V gtg     5 A gcg     0 E gag   101 G ggg     1
      F ttt    10 S tct     8 Y tat     7 C tgt     4
      F ttc    12 S tcc     2 Y tac     4 C tgc     3
      L tta     6 S tca     4 * taa     7 * tga    10
      L ttg    11 S tcg     3 * tag     4 W tgg     6
      L ctt     5 P cct     3 H cat     4 R cgt     0
      L ctc     6 P ccc     1 H cac     4 R cgc     0
      L cta     3 P cca     1 Q caa     9 R cga     5
      L ctg     6 P ccg     3 Q cag     5 R cgg     2
      I att    13 T act     6 N aat     7 S agt     4
      I atc     7 T acc     0 N aac     3 S agc     2
      I ata    12 T aca     5 K aaa     9 R aga    16
      M atg     7 T acg     3 K aag     4 R agg     4
      V gtt     6 A gct     2 D gat     8 G ggt     4
      V gtc     2 A gcc     1 D gac     3 G ggc     1
      V gta     5 A gca     1 E gaa     9 G gga     9
      V gtg     4 A gcg     0 E gag     3 G ggg     0

To calculate such a table using spin the following steps are required. First calculate the codon usage for a typical coding segment and save the resulting table in table A. Then use the option again, but this time select to "Output double table", and type the name of table A into the "File name" text box. Next define the start and end points of a non-coding region, and save the results to double table B. The file containing double table B is now suitable for use by the protein gene searching functions.

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This page is maintained by staden-package. Last generated on 22 October 2002.