This is the command oligotm that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
oligotm - Prints oligo's melting temperature on stdout
SYNOPSIS
oligotm [OPTIONS] {oligo}
where oligo is a DNA sequence of between 2 and 36 bases
DESCRIPTION
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.
Use oligotm online using onworks.net services
