Synthetic | Molecula Maxima

Strand Variables are declared using the Strand datatype (~).
Strands may contain raw nucleotide sequences (written as lower case letters, e.g. acgt ).
Strands may contain raw amino acid sequences (written as upper case letters, e.g. ARNDCEQGHILKMFPSTWYV).
Use the arrow <- operator in order to append composites of nucleotide and amino acid sequences into the strand variable.

As seen above, sequences can be grouped by enclosing them with white space or by using parentheses.
Sequences can be multiplied using the multiplication operator xn.

Use the complement ~ operator in order to get the complementary enclosed sequence (a becomes t, t becomes a, g becomes c and c becomes g).

The coding strand is written from the 5′ (5 prime end) to the 3′ (3 prime end).
By default, raw nucleotide or amino acid sequences are written from 5′ to 3′.
You can explicitly specify the sequence direction by flanking the desired sequence either with 5′ and 3′ or with 3′ and 5′.
A sequence flanked with 3′ to 5′ is appended in reverse order.

Plasmid variables work similar to strand variables.
Plasmid variables store 2 strands, one for the plasmid backbone and one for the plasmid insert.
Use the arrow <- operator to append a sequence to the plasmid backbone.
Use the flank U (or u) operator to append a sequence to the plasmid insert.

Synthetic™ supports the following annotations for iGEM genetic parts and devices: promoter, rbs (for ribosome binding site), protein_domain, trans_unit (translational unit), cds (protein coding sequence), composite, terminator, dna, protein_gen (protein generator), reporter, inverter, sender, receiver, measurement_device.
Use curly brackets ‘{‘ ‘}’ in order to flank a sequence, after the annotation declaration: annotation_type { my_sequence }.
Read more about annotations at the iGEM Catalog Of Parts.

Performing a reverse complement to genetic parts (annotations) is easy ! Add ‘r’ at the beginning of each annotation, rannotation_type{my-sequence}.

Strands can also be appended to other strands, by using the reference box operator.
enclose the strand variable name within an opening and a closing bracket [ my_previously_declared_strand ].

Synthetic™ has a built in support for iGEM BioBrick parts.
Use iGEM BioBrick Ids enclosed in quotes and brackets in order to append their sequence.
Databases reference boxes are the right way to use Synthetic™.

Synthetic™ has a built in support for Protein Data Bank (PDB) entries.
Use PDB Ids enclosed in quotes and brackets in order to append their chain sequence.
If not specified otherwise, the first chain is retrieved implicitly.
You can explicitly retrieve a different chain by using the chain letter preceded by the dot ‘.’ operator (both upper case and lower case letters are supported).
Formats: [‘my_pdb_id’] or [‘my_pdb_id.my_chain_id’].
Databases reference boxes are the right way to use Synthetic™.

Synthetic™ has a built in support for NCBI entries.
Use NCBI Version Ids enclosed in quotes and brackets in order to append their corresponding sequence.

Synthetic™ has a built in support for codon usage optimizations for strand, plasmid and file variables.
Use the ‘optimized for (organism_name)’ operator, prior to the arrow <- operator, in order to convert amino acids to the optimized nucleotides representations, during compilation.
Start typing the organism name within the parentheses, press ctrl+space and choose from the popup list the correct organism.

Place different modular functionality in different .cyto files by using the include “file_name.cyto” command.