OLIGOTM(1) | Primer3 User Manuals | OLIGOTM(1) |
NAME¶
oligotm - Prints oligo's melting temperature on stdoutSYNOPSIS¶
oligotm
[OPTIONS] {oligo}
where oligo is a DNA sequence of between 2 and 36 bases
DESCRIPTION¶
OPTIONS¶
-mv monovalent_concConcentration 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 deoxynycleotide 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:
-sc [0..2]
•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.
Specifies salt correction formula for the
melting temperature calculation:
-i
•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.
•1 Owczarzy et al., 2004.
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.SEE ALSO¶
COPYRIGHT¶
Copyright © 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky05/09/2008 | oligotm 1.1.4 |