melting_temperature
Read-only
The melting temperature of an oligo IN A BUFFER, UNDER A MODEL — and the working, not just the number. Nearest-neighbor (SantaLucia & Hicks 2004 · Allawi & SantaLucia 1997 · Sugimoto 1996 · Breslauer 1986), pydna's dsDNA-binding-domain model, the GC formula, the Wallace rule or NEB, over the salt correction you name, then DMSO and formamide depression under the published model you name. LOCKED NUCLEIC ACID is understood: write the probe as it is ordered, with an L after each locked base (GTCGLAACAGC), and McTigue, Peterson & Kahn's (2004) per-neighbor increments are added to the nearest-neighbor sum. Returns the per-step breakdown the panel shows, so a pipeline can read WHICH coefficient produced a ΔTm rather than a bare temperature.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| model | No | which melting model — nn_santalucia (Nearest-neighbor, SantaLucia 1997) · nn_unified (Nearest-neighbor, unified 2004) · nn_sugimoto (Nearest-neighbor, Sugimoto 1996) · nn_breslauer (Nearest-neighbor, Breslauer 1986) · nn_rna_xia (RNA/RNA, Xia 1998) · nn_rna_chen (RNA/RNA, Chen 2012 (GU wobble)) · nn_rna_freier (RNA/RNA, Freier 1986) · nn_hybrid_sugimoto (RNA/DNA hybrid, Sugimoto 1995) · bresluc_dbd (Breslauer (dsDNA-binding polymerase)) · gc (GC-based (Tm_GC)) · wallace (Wallace rule (2·AT + 4·GC)) · neb (NEB). Advanced. | nn_unified |
| oligo | Yes | the oligo to melt, 5'→3'. IUPAC ambiguity codes and whitespace are tolerated; at least 2 bases. An L after a base marks it LOCKED (LNA), e.g. GTCGLAACAGC — the marker is not a base and does not count toward the length. | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| conditions | No | the buffer this temperature is measured in: Na⁺/K⁺/Tris/Mg²⁺/dNTP under `salt`, the strand concentrations under `oligo`, and any DMSO or formamide under `additives`. Left unset it is filled from your reaction-conditions settings, which is what the Melting Temperature panel is showing, so the two doors cannot quote different temperatures for one oligo. Advanced. | |
| dmso_method | No | which published DMSO depression — ahs01 (Ahsen et al. (2001), 0.75 °C per %) · mus81 (Musielski et al. (1981), 0.6 °C per %) · cul76 (Cullen and Bick (1976), 0.5 °C per %) · esc80 (Escara and Hutton (1980), 0.675 °C per %). Only read when the conditions carry DMSO. Only applies when dmso is set. Advanced. | ahs01 |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| gc | Yes | GC content [%] of the oligo, weighted for ambiguity codes | |
| tm | Yes | melting temperature [°C] after every correction the conditions asked for | |
| model | Yes | the model that produced it, named — never the id alone | |
| steps | Yes | the derivation, one row per correction: the base model with its table and salt method, then each additive with the degrees it removed AND the published model that set the coefficient — the same rows the panel prints, from the same generator | |
| baseTm | Yes | the temperature BEFORE any additive, so a pipeline can see what DMSO or formamide cost rather than inferring it | |
| caveat | Yes | why this model's number should not be read for an oligo of this length, or empty when it can be — Wallace above its published 14–20 nt domain is the case this exists for | |
| lockedBases | Yes | how many bases of this oligo were read as LOCKED (LNA). 0 for ordinary DNA, so a pipeline can tell whether McTigue's increments were in play without parsing the steps | |
| thermodynamics | Yes | ΔH, ΔS and ΔG(37 °C) from the SAME table as the temperature, so a row never mixes two models. Absent for models that carry no nearest-neighbor table (GC formula, Wallace, NEB) |