Modules¶
Moclo module classes.
A module is a sequence of DNA that contains a sequence of interest, such as a promoter, a CDS, a protein binding site, etc., organised in a way it can be combined to other modules to create an assembly. This involves flanking that target sequence with Type IIS restriction sites, which depend on the level of the module, as well as the chosen MoClo protocol.
Abstract¶
- class moclo.core.modules.AbstractModule(object)[source]¶
An abstract modular cloning module.
- cutter¶
the enzyme used to cut the target sequence from the backbone plasmid during Golden Gate assembly.
- Type
RestrictionType
- __init__(record)¶
- is_valid()¶
Check if the wrapped record follows the required class structure.
- overhang_end()[source]¶
Get the downstream overhang of the target sequence.
- Returns
the downstream overhang.
- Return type
Seq
- overhang_start()[source]¶
Get the upstream overhang of the target sequence.
- Returns
the downstream overhang.
- Return type
Seq
- classmethod structure()[source]¶
Get the module structure, as a DNA regex pattern.
Warning
If overloading this method, the returned pattern must include 3 capture groups to capture the following features:
The upstream (5’) overhang sequence
The module target sequence
The downstream (3’) overhang sequence
- target_sequence()[source]¶
Get the target sequence of the module.
Modules are often stored in a standardized way, and contain more than the sequence of interest: for instance they can contain an antibiotic marker, that will not be part of the assembly when that module is assembled into a vector; only the target sequence is inserted.
- Returns
the target sequence with annotations.
- Return type
SeqRecord
Note
Depending on the cutting direction of the restriction enzyme used during assembly, the overhang will be left at the beginning or at the end, so the obtained record is exactly the sequence the enzyme created during restriction.
Level -1¶
Level 0¶
Level 1¶
- class moclo.core.modules.Cassette(AbstractModule)[source]¶
A level 1 module, also refered as a Transcriptional Unit.
Cassettes can either express genes in their target organism, or be assembled into multigene modules for expressing many genes at once, depending on the chosen cassette vector during level 0 assembly.
Level 2¶
- class moclo.core.modules.Device(AbstractModule)[source]¶
A level 2 module, also refered as a Multigene plasmid.
Modules of this level are assembled from several transcriptional units so that they contain several genes that can be expressed all at once. Most of the MoClo implementations are designed so that multiple devices can be assembled into a module that is also a valid level 1 module, as does the Golden Braid system with its α and Ω plasmids.