Difference between revisions of "Help:Assembly Compatibility"
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| + | ==Assembly Compatability== | ||
| + | The Registry supports several standards: users can work with the assembly standard and techniques of their choice. However, all parts submitted to the Registry must be BioBrick compatible. | ||
===How is a part compatible?=== | ===How is a part compatible?=== | ||
Revision as of 20:07, 13 June 2014
Add a Part to the Registry: Related Registry Help Pages
- Add a Basic Part - A tutorial on how to add a basic part
- Add a Composite Part - A tutorial on how to add a composite part
- Scars - Information on assembly scars, and how to specify them for a composite part
- Synthesis - Things to keep in mind if you're adding and documenting a part you've synthesized
- Assembly Compatibility - Make sure your part is compatible with an assembly standard
- Twins - Parts are twins if they have the same sequence
- Document Parts - Recommendations on how to document your parts
- Make a Contribution - Improve existing parts
Have questions on adding a part to the Registry? Send an email to hq (at) igem . org.
Assembly Compatability
The Registry supports several standards: users can work with the assembly standard and techniques of their choice. However, all parts submitted to the Registry must be BioBrick compatible.
How is a part compatible?
The part's sequence must not contain illegal restriction sites (or other specified sequences) as defined by the assembly standard.
BioBrick compatible parts must not have the following restriction sites:
| Sequence | Type | Enzyme | Note |
|---|---|---|---|
| gaattc | Illegal | EcoRI | |
| tctaga | Illegal | XbaI | |
| actagt | Illegal | SpeI | |
| ctgcag | Illegal | PstI | |
| gcggccgc | Avoid | NotI |
All of these restriction sites belong to the prefix and suffix of the BioBrick assembly standard.
Supported Standards
By supporting an assembly standard, the Registry software can detect and understand the assembly process for parts. This includes:
- Detection of illegal restriction sites in a part's sequence
- Recognizing assembly scars in composite parts
- Identification of a sample's assembly standard, through sequence verification of the sample's prefix and suffix
- Remember, a part can have many samples in the Registry's Repository. Those samples can be in plasmid backbones of different assembly standards.
View the Assembly Systems Page to see exactly what the Registry software looks for in these supported assembly standards
Click below to view the supported assembly standards as specified by their original RFC
- 10 - BioBrick - [http://dspace.mit.edu/handle/1721.1/45138 RFC Documentation]
- 12 - BioBrick 2 - [http://dspace.mit.edu/handle/1721.1/45139 RFC Documentation]
- 21 - Berkeley/BglBricks - [http://dspace.mit.edu/handle/1721.1/46747 RFC Documentation]
- 23 - Silver Standard - [http://dspace.mit.edu/handle/1721.1/32535 RFC Documentation]
- 25 - Freiburg Standard - [http://dspace.mit.edu/handle/1721.1/45140 RFC Documentation]
- 1000 - MoClo
Why is compatibility important?
iGEM and the Registry is built on Standard Biological Parts.
- Compatibility ensures that a user can use the part with said assembly standard.
- BioBrick compatible parts ensure that all teams can assemble parts with 3A Assembly, in addition to other assembly techniques
My part is not BioBrick compatible
Before working with your part in the lab (characterizing/measuring), make sure it is BioBrick compatible. If not...
- Synthesize your part to remove any illegal restriction sites, through synonymous substitutions (silent mutations).
- Synthesis is also useful, since you can synthesize your part with the BioBrick prefix and suffix, so it is ready for shipping to the Registry. See our synthesis offer with IDT
- Use site-specific mutagenesis to remove any illegal restriction sites, through synonymous substitutions (silent mutations).