Primers & oligos

Primer designer

De-novo PCR primer design (Primer3-style penalty picker): enumerate and score candidate primer pairs against length/Tm/GC/3'-clamp/structure constraints.

post/primer_design

Request

  • Base URL: https://seqbench.com/api/v1
  • URL: https://seqbench.com/api/v1/primer_design
  • Auth: none required

Request body

templatestring required

Nucleotide sequence (raw or FASTA; IUPAC accepted).

lenMininteger
lenOptinteger
lenMaxinteger
tmMinnumber
tmOptnumber
tmMaxnumber
tmMaxDiffnumber

Max Tm difference within a pair (°C).

gcMinnumber
gcMaxnumber
ampliconMininteger
ampliconMaxinteger
targetStartinteger

1-based inclusive start of a region the product must span (optional).

targetEndinteger

1-based inclusive end of the target region (optional).

maxReturninteger

Number of best pairs to return.

maxPolyXinteger

Longest run of one base a primer may contain (Primer3's PRIMER_MAX_POLY_X). Omitted or 0 means no limit.

gcClampinteger

Consecutive G/C required at the very 3' end (Primer3's PRIMER_GC_CLAMP). Omitted or 0 means no requirement.

minThreePrimeDGnumber

Floor on the NN ΔG37 (kcal/mol) of the five 3'-most bases; a more stable end than this is rejected. Deliberately not Primer3's max_end_stability, which is a different scale this model has not been calibrated against.

oligoNMnumber

Total strand concentration (nM).

naMMnumber

Monovalent cation [Na+]/[K+] (mM).

mgMMnumber

Divalent cation [Mg2+] (mM).

dntpMMnumber

Total [dNTP] (mM), chelates Mg2+.

Response

Tool ran successfully.

okunknown required
toolstring required

The tool slug that ran.

resultobject required

Tool-specific output object. Its shape depends on the tool — call GET /{tool} or see the docs for each tool's fields.

Example response

{
  "provenance": {
    "apiVersion": "1.1.0"
  }
}

Changes

No recorded changes to this operation across all 1 revision of this API.