Target organisms

Currently, GIL supports Saccharomyces Cerevisiae (baker’s yeast), Pichia, E.coli, and Humans as compilation targets.

To specify a target, use #target Organism. GIL also supports using multiple names for the same organism. To add a name for an organism, add the organism’s name.gilEncoding to the CompilationTargets folder. Add goto the name of the file with the full codon encodings for the organism.

Example:

goto S.cerevisiae

Organism names

Saccharomyces Cerevisiae

Saccharomyces cerevisiae, S.cerevisiae, Yeast

Pichia

Pichia pastoris, Pichia

E.Coli

E.coli, Escherichia coli

Human

Human

Adding support for other organisms

GIL stores codon encodings in .gilEncoding files in the CompilationTargets folder. To add support for another organism, add the file organism name.gilEncoding to the CompilationTargets folder. In this file, add the lower case single letter abreviation of the amino acid and its associated codons in order of codon availability, seperated by a colon.

That was hard to describe, so here’s an example for baker’s yeast:

g : GGT GGA GGC GGG