melting_temperature
Read-only
The melting temperature of an oligo IN A BUFFER, UNDER A MODEL — and the working, not just the number.
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) |