DNA Hybridization Melting Temperature Open Source

Question

[Michele Busby]

Hi,

Is there a good open source software for calculating the melting temperature of two DNA sequences?

I have been trying the Biopython MeltingTemp module but it relies on tables for the possible mismatches and many of the possible mismatches are not in the tables, so my sequences get kicked out. The Melting program at the EBI seems to be kicking out a lot of sequences too.

Or is there a way to get these to work? There are a lot of academic software but it is usually a huge hassle to get a commercial license.

Thank you!

Michele

[microfuge]

How about EMBOSS suite ?

Answer 1

[Pierre Lindenbaum]

the standlone tool oligotm in primer3

USAGE: /home/lindenb/package/primer3-2.3.5/src/oligotm OPTIONS oligo

where oligo is a DNA sequence of between 2 and 36 bases

and

OPTIONS can include any of the the following:

-mv monovalent_conc - concentration of monovalent cations in mM, by default 50mM

-dv divalent_conc   - concentration of divalent cations in mM, by default 0mM

-n  dNTP_conc       - concentration of deoxynycleotide triphosphate in mM, by default 0mM

-d  dna_conc        - concentration of DNA strands in nM, by default 50nM

-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 parameters 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 VAULE*
                  2  Owczarzy et al., 2004

source: https://github.com/primer3-org/primer3/blob/master/src/oligotm.c

[Michele Busby]

Thank you Pierre! That did the trick