How much homology do the fragment ends need?

The overlap requirement is a setting on the run, so a join can be evaluated at the homology length your assembly protocol actually uses. Fragments that do not meet it are reported as unfused rather than forced together.

Can I fuse more than two fragments?

Yes. The product keeps the leaf parts it was assembled from, so a three-fragment or four-fragment join can still be read back to the fragment that supplied each stretch.

Does the fused product keep the annotations?

Features from the source fragments are carried onto the product at their new coordinates, and the product can be opened as its own project to continue working on it.

Amplify · experimental

Fusion PCR

Collect the fragments you intend to join, from the open sequence, the current selection or pasted bases, and fuse the ones whose ends actually overlap. The result is the real fused molecule, with the leaf parts it was built from still identified, not a diagram of the intended join.

Open Fusion PCR Open the Primer test sample

Real sequences (GenBank plasmid, FASTA, and a protein family) for the Primer Designer

What it does

01Fragments taken from the open sequence, the current selection, or pasted bases
02Fusion by shared terminal homology, with the fragments that cannot join reported as such
03The fused product with its length, GC and product melting temperature
04The leaf parts of the fusion kept, so a multi-fragment join is traceable to its inputs
05Features carried onto the product from the fragments that supplied them
06A virtual gel of the product, and the product opened as a new project or downloaded

What it runs on

Fusion runs on the `@ports/fusion` port of pydna `fuseByPcr`, validated against pydna. The panel runs on @ports/fusion, @ports/gel, @ports/multiplex, @ports/pcr, @ports/primer.

Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.

Questions

How much homology do the fragment ends need?: The overlap requirement is a setting on the run, so a join can be evaluated at the homology length your assembly protocol actually uses. Fragments that do not meet it are reported as unfused rather than forced together.
Can I fuse more than two fragments?: Yes. The product keeps the leaf parts it was assembled from, so a three-fragment or four-fragment join can still be read back to the fragment that supplied each stretch.
Does the fused product keep the annotations?: Features from the source fragments are carried onto the product at their new coordinates, and the product can be opened as its own project to continue working on it.

Also searched as

overlap extension PCR · fusion PCR simulator · SOE PCR design · splice by overlap extension · join dna fragments in silico · seamless fusion pcr tool · SOEing PCR design · gene fusion by PCR · chimeric gene construction · fusion protein construct design