oligotm1

Usage

Overview

oligotm prints the melting temperature of a given deoxyribonucleotide on the standard output. It is part of the oligotm library.

Options

-mv monovalent_conc

Concentration of monovalent cations in mM, by default 50 mM.

-dv divalent_conc

Concentration of divalent cations in mM, by default 0 mM.

-n dNTP_conc

Concentration of deoxynucleotide triphosphate in mM, by default 0 mM.

-d dna_conc

Concentration of DNA strands in nM, by default 50 nM.

-tp [0|1]

Specifies the table of thermodynamic parameters and the method of melting temperature calculation:

• 0 Breslauer et al., 1986 and Rychlik et al., 1990 (used by primer3 up to and including release 1.1.0). This is the default, but not the recommended value.

• 1 Use nearest neighbor parameter from SantaLucia 1998. This is the recommended value.

-sc [0..2]

Specifies salt correction formula for the melting temperature calculation:

• 0 Schildkraut and Lifson 1965, used by primer3 up to and including release 1.1.0. This is the default, but not the recommended value.

• 1 SantaLucia 1998. This is the recommended value.

• 2 Owczarzy et al., 2004.

-i

prints references to publications which were used for thermodynamic calculations.

Reference

Please cite Rozen, S., Skaletsky, H. "Primer3 on the WWW for general users and for biologist programmers." In S. Krawetz and S. Misener, eds. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology. Humana Press, Totowa, NJ, 2000, pages 365-386.