From plasmid map to verified clone
Open a construct, check its features and translations, plan digests on a virtual gel, check primers under your real buffer, and read Sanger traces against the reference — with every number explained, and every guess labelled as one.
Your analyses
Construct
A plasmid or linear construct: map, features with CDS translation checks, restriction analysis with every commercially available enzyme, a virtual digest on an agarose gel, and a six-frame ORF scan.
Enzymes: every commercially available enzyme in REBASE as shipped with Biopython (no internet needed). An .ab1 trace dropped here is sent to the Sanger tool's slot instead.
Primers
Melting temperature by three methods under the buffer you actually use, composition and 3′ checks, a transparent complementarity check for dimers and hairpins, pair analysis, and a virtual PCR on a template.
Sanger
Load one or more .ab1 traces and the reference they should match. Each read is quality-trimmed, aligned on both strands, and every difference is called with a confidence — then the reads are combined into an answer to “is my clone fully sequence-verified?”.
Quality: Phred Q20 = 1 error in 100 bases, Q30 = 1 in 1,000. A difference is only called confident at Q ≥ 30 with good neighbours; everything below is labelled for what it is.
Protein
A protein sequence, DNA to translate, or a CDS from a loaded construct: mass, pI, charge, extinction coefficient and an A280 → mg/mL converter, hydropathy, composition, tags and protease sites with the scar they leave.
Design primers
Primers for a feature or a region of a construct: PCR pairs scored like primer3, cloning primers anchored on the insert with restriction-site tails, or a walk of sequencing primers. Each design is judged by the same Tm, clamp, dimer and off-target checks as the Primers tool, under your buffer.
Scoring is primer3-style (penalties from the ideal) but it is not primer3 and computes no ΔG for dimers or hairpins; the weights are printed under each result. Check a chosen pair in the Primers tool to see its virtual PCR.
Sequence tools
Reverse complement, translation in any NCBI genetic code, IUPAC motif search on both strands, and a SEGUID checksum that also recognises the same circular plasmid written from another starting point.