dan
Function
Description
Dan calculates the melting temperature (Tm) and the percent G+C of a
nucleic acid sequence (optionally plotting them). For the Melting
temperature profile, free energy values calculated from nearest neighbor
thermodynamics are used (Breslauer et al. Proc. Natl. Acad. Sci.
USA 83, 3746-3750 and Baldino et al. Methods in Enzymol. 168,
761-777).
Usage
Command line arguments
Input file format
Any DNA or RNA sequence USA.
Output file format
If a plot is not being produced, dan reports the sequence of each
oligomer window, its melting temperature under the specified conditions
and its GC content.
By default dan writes a 'seqtable' report file.
The header information contains details of the program, date and sequence
Subsequent lines contain columns of data for each window into the
sequence as it is moved along, giving:
- The start postion of the window
- The end position of the window
- The melting temperature of the window
- The percentage C+G of the window
- The sequence of the window
If the qualifier '-product' is used to make the program prompt for
percent formamide percent of mismatches allowed and product length, then
the output includes the melting temperature of the specified product.
If the qualifier '-thermo' is gived then the DeltaG, DeltaH and DeltaS
of the sequence in the window is also output.
Data files
The EMBOSS data files "Edna.melt" and "Erna.melt" are used to read in the
entropy/enthalpy/energy data for DNA and RNA respectively.
Notes
None.
References
-
Breslauer, K.J., Frank, R., Blocker, H., and Marky, L.A. (1986).
"Predicting DNA Duplex Stability from the Base Sequence." Proceedings of
the National Academy of Sciences USA 83, 3746-3750.
-
Baldino, M., Jr. (1989). "High Resolution In Situ Hybridization
Histochemistry." In Methods in Enzymology, (P.M. Conn, ed.), 168,
761-777, Academic Press, San Diego, California, USA.
Warnings
RNA sequences must be submited to this application with the '-rna'
qualifier on the command line, otherwise the sequence will be assumed to
be DNA.
Diagnostic Error Messages
None.
Exit status
0 if successful.
Known bugs
None.
Author(s)
This program was originally included in EGCG under the names "MELT"
and "MELTPLOT", written by
This application was written by
History
Target users
Comments