Hairpin Tm Estimate
Estimate primer hairpin stability by searching the sequence against its own reverse complement for the longest internal inverted-repeat stem of three to eight non-overlapping bases and applying the Wallace rule of four degrees per GC pair and two per AT pair.
Description
Estimate primer hairpin stability by searching the sequence against its own reverse complement for the longest internal inverted-repeat stem of three to eight non-overlapping bases and applying the Wallace rule of four degrees per GC pair and two per AT pair.
Hairpin Tm Estimate is a focused biology tool that estimate primer hairpin stability by searching the sequence against its own reverse complement for the longest internal inverted-repeat stem of three to eight non-overlapping bases and applying the Wallace rule of four degrees per GC pair and two per AT pair. It calculates locally from the values you enter and exposes the result without changing the source observations.1
When to use Hairpin Tm Estimate
Use Hairpin Tm Estimate when you need to estimate primer hairpin stability by searching the sequence against its own reverse complement for the longest internal inverted-repeat stem of three to eight non-overlapping bases and applying the Wallace rule of four degrees per GC pair and two per AT pair. Enter Sequence using the definitions and units below so the result can be reproduced.
- Sequence
- Primer sequence using only uppercase A, C, G and T.
How Hairpin Tm Estimate calculates the result
The published tool contract uses this rule: Estimate primer hairpin stability by searching the sequence against its own reverse complement for the longest internal inverted-repeat stem of three to eight non-overlapping bases and applying the Wallace rule of four degrees per GC pair and two per AT pair.
- Stem length
- Length in bases of the longest non-overlapping internal inverted-repeat stem, or zero when no hairpin stem exists.
- Hairpin temperature
- Wallace-rule melting temperature of the stem in degrees Celsius, or zero without a stem.
Limitations of Hairpin Tm Estimate
The output is an estimate tied to the stated model and coefficients; it is not a direct measurement and should retain that label when reported.
Alternative or Complementary measurements
Retain the original Sequence values and their units alongside the result. Primer Hairpin Risk is useful when you instead need to heuristic primer-hairpin screen that looks for non-overlapping reverse-complementary stems of at least four bases separated by a loop of at least three bases. Self-Dimer Tm Risk provides another view by helping you screen a primer for self-dimer risk by aligning it with its reverse complement, finding the longest contiguous complementary run, and flagging runs of at least five bases.
References
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Primer (molecular biology) — Wikipedia contributors
Similar or alternative tools
- Primer Hairpin Risk
Heuristic primer-hairpin screen that looks for non-overlapping reverse-complementary stems of at least four bases separated by a loop of at least three bases.
- Self-Dimer Tm Risk
Screen a primer for self-dimer risk by aligning it with its reverse complement, finding the longest contiguous complementary run, and flagging runs of at least five bases.
- Nearest Neighbor Tm Approx
Approximate primer melting temperature with a salt-adjusted nearest-neighbor style formula.