Brace Expansion of the biochemical reaction
This paragraph applies to the case that the Metannogen is used for
reconstruction of metabolic networks but not for the annotation of
SBML files.
Some enzymes and transport carriers are unspecific. To avoid
creation of many similar datasets,
can be used.
Brace expansion allows to define several similar biochemical
conversions within one single text string.
If the reaction string entered by the curator contains curly braces
then Metannogen applies Brace expansion to determine the set of
reactions resulting from the dataset.
The result are several biochemical reactions each having a
different metabolite from the group enclosed in curly braces.
The number of resulting equations is the number of metabolites within braces.
If there are several groups of metabolites enclosed in braces then every
i-th metabolite within each group belongs together.
If the number of elements is not the same in all groups then an error
message is written out.
Example for transport reaction
{ Alanine Proline Glutamine }@cyto <=> { Alanine Proline Glutamine }@mito
is expanded to
Alanine@cyto <=> Alanine@mito
Proline@cyto <=> Proline@mito
Glutamine@cyto <=> Glutamine@mito
Example for transaminase reaction
{Alanine Aspartate} + Alpha-Ketoglutarate <=> { Pyruvate Oxalacetate} + Glutamate
is expanded to
Alanine + Alpha-Ketoglutarate <=> Pyruvate + Glutamate
Aspartate + Alpha-Ketoglutarate <=> Oxalacetate + Glutamate
If the second parenthetical group is identical to the first one, then it can be abbreviated by "{}".
This is usually the case for transport reactions.
There must not
be space between both braces:
{ Alanine Proline Glutamine }@cyto <=> {}@mito
Advanced: Double brace expansion: A second independent group of metabolites can be included in double curly {{ ... }} brackets. The
number of resulting reactions corresponds to the ct of the two sets.