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Melt calculates the melting temperature (Tm) and the percent G+C of a nucleic acid sequence using the algorithms described by Breslauer et al. Proc. Natl. Acad. Sci. USA 83, 3746-3750 and Baldino et al. Methods in Enzymol. 168, 761-777.


Melt produces melting temperature and %C + %G profiles. For the melting temperature profile free energy values calculated from nearest neighbour thermodynamics are used (Breslauer et al. Proc. Natl. Acad. Sci. USA, 83:3746-3750, Baldino et al. Methods in Enzymol. 168:761-777).


This program was written by Rodrigo Lopez S. (E-mail:; Post: Biotechnology Centre of Oslo, PO Box 1125 Blindern, N-0317 Oslo 3, Norway).

All EGCG programs are supported by the EGCG Support Team, who can be contacted by E-mail (


Here is a session with Melt that was used with the first 1000 bases of human low density lipoprotein receptor (GenEMBL:hsldlr), using a window of 21 bases, and a shift of one.

  % melt
    MELT of what nucleotide sequence(s)  ?  GenEmbl:hsldlr02
    What should I call the output file (* hsldlr02.melt *) ?
    What window size   (* 20 *) ?
    What shift increment (* 1 *) ?
    What DNA concentration (nM) (* 50.0 *) ?
    What salt concentration (mM) (* 50.0 *) ?
              Start (* 1 *) ?
              End (* 144 *) ? 50


Here is some of the output file:

  ID   HSLDLR02   standard; DNA; PRI; 144 BP.
  AC   L00336; K02573;
  DT   23-APR-1990 (Rel. 23, Last updated, Version 1)
  DT   23-APR-1990 (Rel. 23, Created)
  DE   Human low density lipoprotein receptor gene, exon 2.
  KW   low density lipoprotein receptor; repetitive sequence. . . .
  Melt of: EM_PR:HSLDLR02 check: 8167  from: 1  to 50
    1 TTTCCTCTCTCTCAGTGGGC  20 Tm=59.5 GC%=55.0
    2 TTCCTCTCTCTCAGTGGGCG  21 Tm=63.0 GC%=60.0
    3 TCCTCTCTCTCAGTGGGCGA  22 Tm=63.6 GC%=60.0
    4 CCTCTCTCTCAGTGGGCGAC  23 Tm=62.5 GC%=65.0
    5 CTCTCTCTCAGTGGGCGACA  24 Tm=61.7 GC%=60.0
    6 TCTCTCTCAGTGGGCGACAG  25 Tm=61.7 GC%=60.0
    7 CTCTCTCAGTGGGCGACAGA  26 Tm=61.7 GC%=60.0
    8 TCTCTCAGTGGGCGACAGAT  27 Tm=61.0 GC%=55.0
    9 CTCTCAGTGGGCGACAGATG  28 Tm=62.0 GC%=60.0
   10 TCTCAGTGGGCGACAGATGT  29 Tm=61.9 GC%=55.0
   11 CTCAGTGGGCGACAGATGTG  30 Tm=62.9 GC%=60.0
   12 TCAGTGGGCGACAGATGTGA  31 Tm=64.0 GC%=55.0
   13 CAGTGGGCGACAGATGTGAA  32 Tm=63.3 GC%=55.0
   14 AGTGGGCGACAGATGTGAAA  33 Tm=61.7 GC%=50.0
   15 GTGGGCGACAGATGTGAAAG  34 Tm=61.7 GC%=55.0
   16 TGGGCGACAGATGTGAAAGA  35 Tm=62.8 GC%=50.0
   17 GGGCGACAGATGTGAAAGAA  36 Tm=61.2 GC%=50.0
   18 GGCGACAGATGTGAAAGAAA  37 Tm=58.9 GC%=45.0
   19 GCGACAGATGTGAAAGAAAC  38 Tm=55.9 GC%=45.0
   20 CGACAGATGTGAAAGAAACG  39 Tm=56.9 GC%=45.0
   21 GACAGATGTGAAAGAAACGA  40 Tm=53.7 GC%=40.0
   22 ACAGATGTGAAAGAAACGAG  41 Tm=52.8 GC%=40.0
   23 CAGATGTGAAAGAAACGAGT  42 Tm=52.8 GC%=40.0
   24 AGATGTGAAAGAAACGAGTT  43 Tm=51.5 GC%=35.0
   25 GATGTGAAAGAAACGAGTTC  44 Tm=52.3 GC%=40.0
   26 ATGTGAAAGAAACGAGTTCC  45 Tm=54.3 GC%=40.0
   27 TGTGAAAGAAACGAGTTCCA  46 Tm=56.9 GC%=40.0
   28 GTGAAAGAAACGAGTTCCAG  47 Tm=55.0 GC%=45.0
   29 TGAAAGAAACGAGTTCCAGT  48 Tm=55.0 GC%=40.0
   30 GAAAGAAACGAGTTCCAGTG  49 Tm=55.0 GC%=45.0
   31 AAAGAAACGAGTTCCAGTGC  50 Tm=57.0 GC%=45.0


MeltPlot is a program that produces a graphical representation of the Tm and %CG profiles.




Melt uses a running window of specified length on which it calculates the melting temperature and the %CG contents.


RNA sequences must be submited to Melt with the -RNA qualifier on the command line. See section on command line parameters.





The input file for Melt is a GCG formatted nucleic acid sequence.


All parameters for this program may be put on the command line. Use the option -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the qualifier names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose qualifiers or parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

  Minimum syntax: % melt [-INfile=]empri:hsldlr -Default
  Prompted Parameters:
  -BEGin=1 -END=1000      the range of interest
  -WINdow=100             the window length
  -SHIFT=1                the window shift
  -DNAConc=50             the DNA concentration (nM)
  -SALTConc=50            the salt concentration (mM)
  [-OUTfile=]hsldlr.melt  output file
  Local Data Files: None
  Optional Parameters:
  -RNA                    the sequence is RNA
  -PRODuct                to ask the following:
  -FORMamide=0.0          the percent formamide
  -MISMatch=0.0           the percent mismatch allowed
  -PRODLength=50          the product length (defaults to window size)




The parameters and switches listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.


sets the parameters for RNA bases rather than DNA.


prompts for percent formamide percent of mismatches allowed and product length.


specifies the percent formamide to be used in calculations (ignored unless -PRODuct is used).


specifies the percent mismatch to be used in calculations (ignored unless -PRODuct is used).


specifies the product length to be used in calculations (ignored unless -PRODuct is used).


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.

Printed: April 22, 1996 15:54 (1162)