Icon Genetics Kit

An implementation of the Icon Genetics ToolKit for the Python MoClo library.

References

  1. Weber, E., Engler, C., Gruetzner, R., Werner, S., Marillonnet, S. (2011). A Modular Cloning System for Standardized Assembly of Multigene Constructs. PLOS ONE, 6(2), e16765.
  2. Werner, S., Engler, C., Weber, E., Gruetzner, R., & Marillonnet, S. (2012). Fast track assembly of multigene constructs using Golden Gate cloning and the MoClo system. Bioengineered, 3(1), 38–43.

Level -1

Module

class moclo.kits.ig.IGProduct(Product)[source]

An Icon Genetics MoClo product.

__init__(record)

Initialize self. See help(type(self)) for accurate signature.

cutter

alias of Bio.Restriction.Restriction.BpiI

is_valid()

Check if the wrapped record follows the required class structure.

Returns:True if the record is valid, False otherwise.
Return type:bool
overhang_end()

Get the downstream overhang of the target sequence.

Returns:the downstream overhang.
Return type:Seq
overhang_start()

Get the upstream overhang of the target sequence.

Returns:the downstream overhang.
Return type:Seq
classmethod structure()

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:

  1. The upstream (5’) overhang sequence
  2. The module target sequence
  3. The downstream (3’) overhang sequence
target_sequence()

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.

Vector

class moclo.kits.ig.IGEntryVector(EntryVector)[source]

An Icon Genetics entry vector.

References

Weber et al., Figure 2A.

__init__(record)

Initialize self. See help(type(self)) for accurate signature.

assemble(module, *modules, **kwargs)

Assemble the provided modules into the vector.

Parameters:
  • module (AbstractModule) – a module to insert in the vector.
  • modules (AbstractModule, optional) – additional modules to insert in the vector. The order of the parameters is not important, since modules will be sorted by their start overhang in the function.
Returns:

the assembled sequence with sequence annotations inherited from the vector and the modules.
Return type:

SeqRecord
Raises:
  • DuplicateModules – when two different modules share the same start overhang, leading in possibly non-deterministic constructs.
  • MissingModule – when a module has an end overhang that is not shared by any other module, leading to a partial construct only
  • InvalidSequence – when one of the modules does not match the required module structure (missing site, wrong overhang, etc.).
  • UnusedModules – when some modules were not used during the assembly (mostly caused by duplicate parts).
cutter

alias of Bio.Restriction.Restriction.BpiI

is_valid()

Check if the wrapped record follows the required class structure.

Returns:True if the record is valid, False otherwise.
Return type:bool
overhang_end()

Get the downstream overhang of the vector sequence.

overhang_start()

Get the upstream overhang of the vector sequence.

placeholder_sequence()

Get the placeholder sequence in the vector.

The placeholder sequence is replaced by the concatenation of modules during the assembly. It often contains a dropout sequence, such as a GFP expression cassette that can be used to measure the progress of the assembly.

classmethod structure()[source]

Get the vector structure, as a DNA regex pattern.

Warning

If overloading this method, the returned pattern must include 3 capture groups to capture the following features:

  1. The downstream (3’) overhang sequence
  2. The vector placeholder sequence
  3. The upstream (5’) overhang sequence
target_sequence()

Get the target sequence in the vector.

The target sequence if the part of the plasmid that is not discarded during the assembly (everything except the placeholder sequence).

Level 0

Module

class moclo.kits.ig.IGEntry(Entry)[source]

An Icon Genetics MoClo entry.

__init__(record)

Initialize self. See help(type(self)) for accurate signature.

cutter

alias of Bio.Restriction.Restriction.BsaI

is_valid()

Check if the wrapped record follows the required class structure.

Returns:True if the record is valid, False otherwise.
Return type:bool
overhang_end()

Get the downstream overhang of the target sequence.

Returns:the downstream overhang.
Return type:Seq
overhang_start()

Get the upstream overhang of the target sequence.

Returns:the downstream overhang.
Return type:Seq
classmethod structure()

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:

  1. The upstream (5’) overhang sequence
  2. The module target sequence
  3. The downstream (3’) overhang sequence
target_sequence()

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.

Vector

class moclo.kits.ig.IGCassetteVector(CassetteVector)[source]

An Icon Genetics cassette vector.

References

Weber et al., Figure 4A.

__init__(record)

Initialize self. See help(type(self)) for accurate signature.

assemble(module, *modules, **kwargs)

Assemble the provided modules into the vector.

Parameters:
  • module (AbstractModule) – a module to insert in the vector.
  • modules (AbstractModule, optional) – additional modules to insert in the vector. The order of the parameters is not important, since modules will be sorted by their start overhang in the function.
Returns:

the assembled sequence with sequence annotations inherited from the vector and the modules.
Return type:

SeqRecord
Raises:
  • DuplicateModules – when two different modules share the same start overhang, leading in possibly non-deterministic constructs.
  • MissingModule – when a module has an end overhang that is not shared by any other module, leading to a partial construct only
  • InvalidSequence – when one of the modules does not match the required module structure (missing site, wrong overhang, etc.).
  • UnusedModules – when some modules were not used during the assembly (mostly caused by duplicate parts).
cutter

alias of Bio.Restriction.Restriction.BsaI

is_valid()

Check if the wrapped record follows the required class structure.

Returns:True if the record is valid, False otherwise.
Return type:bool
overhang_end()

Get the downstream overhang of the vector sequence.

overhang_start()

Get the upstream overhang of the vector sequence.

placeholder_sequence()

Get the placeholder sequence in the vector.

The placeholder sequence is replaced by the concatenation of modules during the assembly. It often contains a dropout sequence, such as a GFP expression cassette that can be used to measure the progress of the assembly.

classmethod structure()[source]

Get the vector structure, as a DNA regex pattern.

Warning

If overloading this method, the returned pattern must include 3 capture groups to capture the following features:

  1. The downstream (3’) overhang sequence
  2. The vector placeholder sequence
  3. The upstream (5’) overhang sequence
target_sequence()

Get the target sequence in the vector.

The target sequence if the part of the plasmid that is not discarded during the assembly (everything except the placeholder sequence).

Parts

class moclo.kits.ig.IGPromoter(IGPart, IGEntry)[source]

An Icon Genetics promoter part.

class moclo.kits.ig.IGUntranslatedRegion(IGPart, IGEntry)[source]

An Icon Genetics 5’ UTR part.

class moclo.kits.ig.IGSignalPeptide(IGPart, IGEntry)[source]

An Icon Genetics signal peptide part.

class moclo.kits.ig.IGCodingSequence(IGPart, IGEntry)[source]

An Icon Genetics CDS part.

class moclo.kits.ig.IGTerminator(IGPart, IGEntry)[source]

An Icon Genetics terminator part.

Level 1

Module

class moclo.kits.ig.IGCassette(Cassette)[source]

An Icon Genetics MoClo cassette.

cutter

alias of Bio.Restriction.Restriction.BpiI

Vector

class moclo.kits.ig.IGDeviceVector(DeviceVector)[source]

An Icon Genetics device vector.

References

Weber et al., Figure 4A.

cutter

alias of Bio.Restriction.Restriction.BpiI

Parts

class moclo.kits.ig.IGEndLinker(IGPart, IGCassette)[source]

An Icon Genetic end linker part.

References

Weber et al., Figure 5.

Level M

Parts

class moclo.kits.ig.IGLevelMVector(IGPart, IGDeviceVector)[source]
cutter

alias of Bio.Restriction.Restriction.BpiI

classmethod structure()[source]

Get the part structure, as a DNA regex pattern.

The structure of most parts can be obtained automatically from the part signature and the restriction enzyme used in the Golden Gate assembly.

Warning

If overloading this method, the returned pattern must include 3 capture groups to capture the following features:

  1. The upstream (5’) overhang sequence
  2. The vector placeholder sequence
  3. The downstream (3’) overhang sequence
class moclo.kits.ig.IGLevelMEndLinker(IGPart, IGCassette)[source]
classmethod structure()[source]

Get the part structure, as a DNA regex pattern.

The structure of most parts can be obtained automatically from the part signature and the restriction enzyme used in the Golden Gate assembly.

Warning

If overloading this method, the returned pattern must include 3 capture groups to capture the following features:

  1. The upstream (5’) overhang sequence
  2. The vector placeholder sequence
  3. The downstream (3’) overhang sequence

Level P

Parts

class moclo.kits.ig.IGLevelPVector(IGPart, IGCassetteVector)[source]
cutter

alias of Bio.Restriction.Restriction.BsaI

classmethod structure()[source]

Get the part structure, as a DNA regex pattern.

The structure of most parts can be obtained automatically from the part signature and the restriction enzyme used in the Golden Gate assembly.

Warning

If overloading this method, the returned pattern must include 3 capture groups to capture the following features:

  1. The upstream (5’) overhang sequence
  2. The vector placeholder sequence
  3. The downstream (3’) overhang sequence
class moclo.kits.ig.IGLevelPEndLinker(IGPart, IGEntry)[source]
cutter

alias of Bio.Restriction.Restriction.BsaI

classmethod structure()[source]

Get the part structure, as a DNA regex pattern.

The structure of most parts can be obtained automatically from the part signature and the restriction enzyme used in the Golden Gate assembly.

Warning

If overloading this method, the returned pattern must include 3 capture groups to capture the following features:

  1. The upstream (5’) overhang sequence
  2. The vector placeholder sequence
  3. The downstream (3’) overhang sequence