R'MES: Generating Family Files

The rmes.gfam program allows to generate family files which can be used with the -f option of the rmes command. However, only families corresponding to degenerated oligonucleotides on the {a,c,g,t,n} alphabet can be generated.

The basic command is :

rmes.gfam [-t <label>] -p <string>

where

-t <label>
specifies the title of the family file (it will be printed as the first line),
-p <string>
specifies the template pattern of the degenerated oligonucleotides. This pattern is composed of
characters from {a,c,g,t,n,#}. When used, the letters a,c,g,t,n indicate fixed bases, whereas the
symbol # indicates that it will be successively replaced by a, c, g then t to produce different
families.

For instance, the -p #n## option will produce the 64 degenerated tetranucleotides having an n in the second position, whereas the -p ####aa template will produce the 256 hexanucleotides ending with aa.

For more details, please refer to the user guide

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Article | by Dr. Radut