first previous next last contents

Set genetic code

This function allows the user to change the genetic used in all the options. The codes are defined as a set of codon tables stored in the directory tables/gcodes distributed with the package. The current list of codes and their codon table file names is shown at the end of this section.

The user interface consists of the dialogue shown below. The user selects the required code by clicking on it, and then clicking "OK" or "OK permanent". The former choice selects the code for immediate use, and the latter also selects it for future uses of the program.


When the dialogue is left the codon table selected will be displayed, as below, in the Output Window.

      F ttt       S tct       Y tat       C tgt      
      F ttc       S tcc       Y tac       C tgc      
      L tta       S tca       * taa       W tga      
      L ttg       S tcg       * tag       W tgg      
      L ctt       P cct       H cat       R cgt      
      L ctc       P ccc       H cac       R cgc      
      L cta       P cca       Q caa       R cga      
      L ctg       P ccg       Q cag       R cgg      
      I att       T act       N aat       S agt      
      I atc       T acc       N aac       S agc      
      M ata       T aca       K aaa       G aga      
      M atg       T acg       K aag       G agg      
      V gtt       A gct       D gat       G ggt      
      V gtc       A gcc       D gac       G ggc      
      V gta       A gca       E gaa       G gga      
      V gtg       A gcg       E gag       G ggg      

The following table shows the list of available genetic codes and the files in which they are stored for use by the package. They were created from genetic code files obtained from the NCBI.

code_1  Standard
code_2  Vertebrate Mitochondrial
code_3  Yeast Mitochondrial
code_4  Coelenterate  Mitochondrial
code_4  Mold Mitochondrial
code_4  Protozoan Mitochondrial
code_4  Mycoplasma
code_4  Spiroplasma
code_5  Invertebrate Mitochondrial
code_6  Ciliate Nuclear
code_6  Dasycladacean Nuclear
code_6  Hexamita Nuclear
code_9  Echinoderm Mitochondrial
code_10 Euplotid Nuclear
code_11 Bacterial
code_12 Alternative Yeast Nuclear
code_13 Ascidian Mitochondrial
code_14 Flatworm Mitochondrial
code_15 Blepharisma Macronuclear

first previous next last contents
This page is maintained by staden-package. Last generated on 22 October 2002.