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Gibthon Construct Designer

Please note that some of the features described here may not yet be fully implemented

Before you can start to put together a construct, you must first collect a library of parts. In the Gibthon Construct Designer, these are known as 'Fragments'.

These are all stored within the GCD, to speed up access and improve reliability. Currently three data sources are supported:

Name Registry of Standard Parts Nucleotide Database Upload
Location partsregistry.org www.ncbi.nlm.nih.gov/ Your hard drive
Description The Registry of Standard Biological Parts has been developed as a repository for the parts generated and used by iGEM. The Nucleotide Database is a collection of sequences run by the NCBI Genbank format files that you have created yourself (eg from ApE).
Identifier Part name (eg BBa_K190015 or pSB1C3) Search query Genbank or FASTA file

Further data sources will be added in the future

Having importer your fragments, you can now use the Construct Designer to build Constructs.

Now you have amassed a library of parts, you can start to design constructs.

In your Construct Library, add a new construct or open an existing one.

When you open a construct, you are presented with four main areas:

Info Settings

Here you can view the name and description of the construct. To edit this information, just click the edit button.

Here you can view the settings associated with this construct. To edit them, click the edit button.

More info on what the settings do is in the next tab

Fragments Summary

This is where you will do they bulk of your editing. Click on a fragment to expand it. You may add, remove, browse and reorder fragments. From each fragment, you may choose a start and end feature that you wish to extract.

This area contains a summary of your construct so far

Once you have designed your construct, you may save and download it in GenBank format from the menubar at the top.

To generate the primers, just click process on the menubar at the top

Setting Description Default
Mg2+ concentration Magnesium salt concentration for use in priming calculations. 1 M
Na+ concentration Sodium salt concentration for use in priming calculations. 0 M
Secondary Structure Safety Margin Priming calculations will be done at this value above the calculated melting temperature. 3°C
Target Annealing Temperature Target Tm for annealing portion of primer. Set to zero to ignore. 50°C
Target Primer Annealing Temperature Target Tm for whole primer. Set to zero to ignore. 60°C
Minimum Overlap Initial length of primer = twice minimum overlap. 20 bp

More settings will be added as they are required

Once they are generated, selecting 'View Primers' will allow you to see your primers in more detail. Any warnings generated from their design can be seen here. These warnings fall into three categories

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