tm_wallace

The Wallace rule is often used as rule of thumb for approximate melting temperature calculations for primers with 14 to 20 nt length.

Accurate calculation of nucleic acid melting temperature (Tm) is fundamental to many molecular biology applications, and this software scales Tm analysis from individual sequences to genome‑wide thermodynamic profiling. This package extends Tm analysis from simple sequence level computation to comprehensive genome-wide thermodynamic profiling. It takes multiple input formats including sequence strings, FASTA files, genomic coordinates. The implementation provides three Tm calculation methods: the Wallace rule (Thein & Wallace, 1986), empirical GC‑content formulas (Marmur, 1962; Schildkraut, 2010; Wetmur, 1991; Untergasser, 2012; von Ahsen, 2001), and nearest‑neighbor thermodynamics (Breslauer, 1986; Sugimoto, 1996; Allawi, 1998; SantaLucia, 2004; Freier, 1986; Xia, 1998; Chen, 2012; Bommarito, 2000; Turner, 2010; Sugimoto, 1995; Allawi, 1997; SantaLucia, 2005; Zuber, 2022; Ghosh, 2020, 2023). Nearest-neighbor parameter sets are provided for DNA, RNA and RNA/DNA hybrid duplexes. These include sets obtained by melting-temperature optimization that are fitted directly at a stated sodium concentration (Weber, 2015; Ferreira, 2019; Basilio Barbosa, 2019; Banerjee, 2020), which replace salt correction rather than being corrected; salt correction is skipped automatically when the requested condition matches the one a set was fitted at. The Zuber (2022) set additionally replaces the single terminal-AU penalty with end terms that depend on the penultimate base pair, applied automatically at both duplex ends. Parameter sets measured under molecular crowding (Ghosh, 2020, 2023) are also provided for DNA and RNA duplexes, so that duplex stability can be evaluated under cell-like rather than dilute-solution conditions. Corrections are otherwise supported for salt ions (SantaLucia, 1996, 1998; Owczarzy, 2004, 2008) and for chemical conditions such as dimethyl sulfoxide and formamide. A compiled C++ core and parallel task partitioning profile the human genome in 3 minutes on a six-core laptop. This package returns result as a GRanges object for interoperability with Bioconductor workflows and downstream multi-omics analyses. Data-level integration reconciles Tm windows with external multi-omics GRanges objects through overlap, nearest-feature, windowed-count, and binned-average strategies, returning a single unified GRanges object ready for downstream analysis. Visualization-level integration renders multiple feature layers as independent concentric tracks on a shared genomic axis, each retaining its native coordinate resolution. Group comparison supports Wilcoxon rank-sum and Student's t-tests with multiple available correction methods for contrasting Tm and other features across region classes.

Junhui Li

TmCalculator

Genome-Wide Nucleic Acid Melting Temperature Profiling and
Multi-Omics Integration

Lihua Julie Zhu

tm_wallace function

<dl><dt>gr_seq</dt>
<dd>Pre-processed sequence(s) in 5' to 3' direction. This should be the output from
to_genomic_ranges() function.</dd>
<dt>ambiguous</dt>
<dd>Ambiguous bases are taken into account to compute the G and C content when ambiguous is TRUE.</dd></dl>

Arguments

The 2 + 4 rule was calibrated on 14 to 20 nt hybridisation probes and
carries no length-dependent, salt-dependent or concentration-dependent
term. Its error therefore grows without bound as sequences lengthen, and
on genome-scale windows it returns a number that is not a melting
temperature in any useful sense: a 200 bp window is reported at several
hundred degrees Celsius.
Sequences longer than 30 nt raise a warning that names
<code>tm_nn</code> as the appropriate alternative. A warning rather than
an error, because the rule stays a legitimate rule of thumb and users who
knowingly apply it outside its calibrated range should not be blocked;
wrap the call in <code><a href="/link/suppressWarnings()?package=TmCalculator&version=1.1.0" data-mini-rdoc="TmCalculator::suppressWarnings()">suppressWarnings()</a></code> in that case.

Length of validity

Author

Calculate the melting temperature using the 'Wallace rule' — tm_wallace

<dl>

<dt>gr_seq</dt>
<dd>Pre-processed sequence(s) in 5' to 3' direction. This should be the output from
to_genomic_ranges() function.</dd>


<dt>ambiguous</dt>
<dd>Ambiguous bases are taken into account to compute the G and C content when ambiguous is TRUE.</dd>

</dl>

The 2 + 4 rule was calibrated on 14 to 20 nt hybridisation probes and
carries no length-dependent, salt-dependent or concentration-dependent
term. Its error therefore grows without bound as sequences lengthen, and
on genome-scale windows it returns a number that is not a melting
temperature in any useful sense: a 200 bp window is reported at several
hundred degrees Celsius.
Sequences longer than 30 nt raise a warning that names
<code>tm_nn</code> as the appropriate alternative. A warning rather than
an error, because the rule stays a legitimate rule of thumb and users who
knowingly apply it outside its calibrated range should not be blocked;
wrap the call in <code><a href='https://rdrr.io/r/base/warning.html'>suppressWarnings()</a></code> in that case.

tm_wallace: Calculate the melting temperature using the 'Wallace rule'

Description

Usage

Value

Arguments

Length of validity

Author

References

Examples