GG Assembler
 
Paste a sequence, pick a part type, and it designs the primers that make it a part plasmid.
Pick a template from the library or paste a sequence, then set the range and the part type you want. With a library template the Region list is filled from that file's own annotations — pick the CDS and the coordinates fill themselves, so you never have to look them up elsewhere. The primer tails are colour-coded: pad, the cloning enzyme (BbsI for the ccdB vectors), the overhang the destination accepts, BsaI (which releases the part later), and the type's own flank. The destination decides how much the primer carries. A universal ccdB vector always takes the same ends, so the insert brings its own BsaI sites and the type is set by them. A vector already cut for one type, or a part plasmid being reopened, supplies those sites itself — much shorter primers. Internal BsaI, BsmBI, BbsI and NotI sites are always found and always reported, with the single base change that would remove each one. Applying them is opt-in: in a promoter or terminator no change is truly silent, so the call is yours. When removal is on and a site is too far from either end for a primer to reach, the amplicon is split and the two primers meeting at that junction spell the corrected bases. gBlock and Oligo duplex give the same insert without PCR. The predicted plasmid is fed back through the detector, and the page only reports success if it classifies as the type you asked for.
Insert
Sequence conventions
Off by default: in a promoter or terminator no base change is truly silent, so the scan reports what it would do and leaves the call to you.
Generated primer tails
choose a template or paste a sequence
Primers on the template
nothing designed yet
Domestication scan
nothing scanned yet
Destination backbone
Enzyme—
Selection—
Fragments—
Predicted part plasmid
nothing designed yet
What goes in
How it ligates