New Golden Gate Assembly

Generate a Golden Gate assembly design by providing the information below...

General Info

Restriction Enzyme: BsaI
Ligase: T4-DNA

Title

Enter a useful title for this assembly.

Title:

Backbone

Upload a .fasta file containing a single entry of your backbone sequence.

Backbone file:

Insert

Is this a multi-sequence query?

Multi-sequence:

Yes

If you did not select multi-sequence query, upload a .fasta file containing a single sequence entry of your full insert sequence.
If you selected multi-sequence query, upload a .fasta file containing multiple sequence entries that will compose your construct.

Insert file:

Overhangs

Which high-fidelity overhang set will you use for your experiment?

Overhangs set:

- Potapov et al 2018 Go to paper...

Would you like scarless primer design?

Scarless:

Yes

BLAST Query

Which BLAST databases would you like to query from to find parts?

Databases:

AddGene

DNASU

iGEM

Enter the minimum and maximum nucleotide sequence sizes to use that are returned from the database(s). BLAST alignment query results are filtered according to these sizes.

Min BLAST seq size (nt):

Max BLAST seq size (nt):

Enter the minimum and maximum nucleotide sequence sizes to use for synthesized assembly sequences.

Min synthetic seq size (nt):

Max synthetic seq size (nt):

Experiment

Enter experimental parameters you will be using for your assembly experiment in the lab. These values are important for primer desing and thermodynamic analysis.

Monovalent ion concentration (mM):

Divalent ion concentration (mM):

dNTP ion concentration (mM):

DNA concentration (nM):

Melting temperature (℃):

℃

Cost

Enter values for costs of aspects of your assembly experiment.

Nucleotides

Oligo cost ($):

Block cost ($):

Mega block cost ($):

Enzymes

Which enzymes do you need to purchase?

Please input: the total price for a tube of enzyme and the number of reactions per tube.

Master mix?

PCR Polymerase

BsaI

Ligase

Solution Ranking

Enter values for how solutions are ranked based on your weight of considerations of number of parts and assembly cost.

Parts count preference:

Cost preference:

Experimental Probabilities

Enter values for your expected experimental probabilities of success.

PCR probability of success:

P_success

One-pot digestion-ligation probability of success:

P_success