
                                    dan 



Function

   Calculates nucleic acid melting temperature

Description

   Dan calculates the melting temperature (Tm) and the percentage of G+C
   nucleotides for windows over a nucleic acid sequence, optionally
   plotting them. If a plot is not being produced, dan reports the
   sequence of each oligomer window, its melting temperature under the
   specified conditions and its percentage GC content. The change in
   enthalpy (H), entropy (S) and Gibbs free energy (S) for dissociation
   of the oligomers may (optionally) be reported to file (but not
   plotted).

Algorithm

   The values of melting point and other thermodynamic properties of the
   sequence, namely change in enthalpy (H), entropy (S) and Gibbs free
   energy (S) on dissociation, are calculated for a sequence region (or
   "window") of a user-specified size (see "-windowsize" option). The
   window is incrementally moved along the sequence with the properties
   being calculated at each new position. The user must provide the salt
   and DNA concentration. Optionally, the percent formamide, percent of
   mismatches allowed and product length may be specified.

   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

   Here is a sample session with dan


% dan 
Calculates nucleic acid melting temperature
Input nucleotide sequence(s): tembl:x13776
Enter window size [20]: 
Enter Shift Increment [1]: 
Enter DNA concentration (nM) [50.]: 
Enter salt concentration (mM) [50.]: 
Output report [x13776.dan]: 

   Go to the input files for this example
   Go to the output files for this example

   Example 2

   An example of producing a plot of Tm:


% dan -plot -graph cps 
Calculates nucleic acid melting temperature
Input nucleotide sequence(s): tembl:x13776
Enter window size [20]: 
Enter Shift Increment [1]: 
Enter DNA concentration (nM) [50.]: 
Enter salt concentration (mM) [50.]: 
Enter minimum temperature [55.]: 

Created dan.ps

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
   -windowsize         integer    [20] The values of melting point and other
                                  thermodynamic properties of the sequence are
                                  determined by taking a short length of
                                  sequence known as a window and determining
                                  the properties of the sequence in that
                                  window. The window is incrementally moved
                                  along the sequence with the properties being
                                  calculated at each new position. (Integer
                                  from 1 to 100)
   -shiftincrement     integer    [1] This is the amount by which the window
                                  is moved at each increment in order to find
                                  the melting point and other properties along
                                  the sequence. (Integer 1 or more)
   -dnaconc            float      [50.] Enter DNA concentration (nM) (Number
                                  from 1.000 to 100000.000)
   -saltconc           float      [50.] Enter salt concentration (mM) (Number
                                  from 1.000 to 1000.000)
*  -mintemp            float      [55.] Enter a minimum value for the
                                  temperature scale (y-axis) of the plot.
                                  (Number from 0.000 to 150.000)
*  -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tekt, tek, none, data, xterm, png, gif)
*  -outfile            report     [*.dan] If a plot is not being produced then
                                  data on the melting point etc. in each
                                  window along the sequence is output to the
                                  file.

   Additional (Optional) qualifiers (* if not always prompted):
   -product            toggle     This prompts for percent formamide, percent
                                  of mismatches allowed and product length.
*  -formamide          float      [0.] This specifies the percent formamide to
                                  be used in calculations (it is ignored
                                  unless -product is used). (Number from 0.000
                                  to 100.000)
*  -mismatch           float      [0.] This specifies the percent mismatch to
                                  be used in calculations (it is ignored
                                  unless -product is used). (Number from 0.000
                                  to 100.000)
*  -prodlen            integer    [Window size (20)] This specifies the
                                  product length to be used in calculations
                                  (it is ignored unless -product is used).
                                  (Any integer value)
   -thermo             toggle     Output the DeltaG, DeltaH and DeltaS values
                                  of the sequence windows to the output data
                                  file.
*  -temperature        float      [25.] If -thermo has been specified then
                                  this specifies the temperature at which to
                                  calculate the DeltaG, DeltaH and DeltaS
                                  values. (Number from 0.000 to 100.000)

   Advanced (Unprompted) qualifiers:
   -rna                boolean    This specifies that the sequence is an RNA
                                  sequence and not a DNA sequence.
   -plot               toggle     If this is not specified then the file of
                                  output data is produced, else a plot of the
                                  melting point along the sequence is
                                  produced.

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-graph" associated qualifiers
   -gprompt            boolean    Graph prompting
   -gdesc              string     Graph description
   -gtitle             string     Graph title
   -gsubtitle          string     Graph subtitle
   -gxtitle            string     Graph x axis title
   -gytitle            string     Graph y axis title
   -goutfile           string     Output file for non interactive displays
   -gdirectory         string     Output directory

   "-outfile" associated qualifiers
   -rformat            string     Report format
   -rname              string     Base file name
   -rextension         string     File name extension
   -rdirectory         string     Output directory
   -raccshow           boolean    Show accession number in the report
   -rdesshow           boolean    Show description in the report
   -rscoreshow         boolean    Show the score in the report
   -rstrandshow        boolean    Show the nucleotide strand in the report
   -rusashow           boolean    Show the full USA in the report
   -rmaxall            integer    Maximum total hits to report
   -rmaxseq            integer    Maximum hits to report for one sequence

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Input file format

   Any DNA or RNA sequence USA.

  Input files for usage example

   'tembl:x13776' is a sequence entry in the example nucleic acid
   database 'tembl'

  Database entry: tembl:x13776

ID   X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP.
XX
AC   X13776; M43175;
XX
DT   19-APR-1989 (Rel. 19, Created)
DT   14-NOV-2006 (Rel. 89, Last updated, Version 24)
XX
DE   Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
XX
KW   aliphatic amidase regulator; amiC gene; amiR gene.
XX
OS   Pseudomonas aeruginosa
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC   Pseudomonadaceae; Pseudomonas.
XX
RN   [1]
RP   1167-2167
RA   Rice P.M.;
RT   ;
RL   Submitted (16-DEC-1988) to the EMBL/GenBank/DDBJ databases.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG
.
XX
RN   [2]
RP   1167-2167
RX   DOI; 10.1016/0014-5793(89)80249-2.
RX   PUBMED; 2495988.
RA   Lowe N., Rice P.M., Drew R.E.;
RT   "Nucleotide sequence of the aliphatic amidase regulator gene of Pseudomona
s
RT   aeruginosa";
RL   FEBS Lett. 246(1-2):39-43(1989).
XX
RN   [3]
RP   1-1292
RX   PUBMED; 1907262.
RA   Wilson S., Drew R.;
RT   "Cloning and DNA seqence of amiC, a new gene regulating expression of the
RT   Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC
RT   product.";
RL   J. Bacteriol. 173(16):4914-4921(1991).
XX
RN   [4]
RP   1-2167
RA   Rice P.M.;
RT   ;
RL   Submitted (04-SEP-1991) to the EMBL/GenBank/DDBJ databases.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG
.
XX
DR   GOA; Q51417.
DR   UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE.
XX


  [Part of this file has been deleted for brevity]

FT                   /replace=""
FT                   /note="ClaI fragment deleted in pSW36,  constitutive
FT                   phenotype"
FT   misc_feature    1
FT                   /note="last base of an XhoI site"
FT   misc_feature    648..653
FT                   /note="end of 658bp XhoI fragment, deletion in  pSW3 cause
s
FT                   constitutive expression of amiE"
FT   conflict        1281
FT                   /replace="g"
FT                   /citation=[3]
XX
SQ   Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other;
     ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat        6
0
     ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac       12
0
     aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg       18
0
     aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg       24
0
     agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc       30
0
     ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg       36
0
     tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg       42
0
     agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga       48
0
     acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga       54
0
     ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa       60
0
     gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct       66
0
     acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg       72
0
     cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg       78
0
     ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg       84
0
     aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt       90
0
     acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct       96
0
     tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc      102
0
     tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt      108
0
     acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca      114
0
     gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc      120
0
     agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt      126
0
     ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg      132
0
     cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca      138
0
     gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt      144
0
     gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc      150
0
     gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc      156
0
     cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga      162
0
     tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa      168
0
     gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca      174
0
     ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct      180
0
     gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg      186
0
     aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt      192
0
     catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg      198
0
     gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct      204
0
     gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa      210
0
     ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt      216
0
     cctcgag                                                                216
7
//

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.

   The output is a standard EMBOSS report file.

   The results can be output in one of several styles by using the
   command-line qualifier -rformat xxx, where 'xxx' is replaced by the
   name of the required format. The available format names are: embl,
   genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel,
   feattable, motif, regions, seqtable, simple, srs, table, tagseq

   See: http://emboss.sf.net/docs/themes/ReportFormats.html for further
   information on report formats.

   By default dan writes a 'seqtable' report file.

  Output files for usage example

  File: x13776.dan

########################################
# Program: dan
# Rundate: Tue 15 Jul 2008 12:00:00
# Commandline: dan
#    -sequence tembl:x13776
# Report_format: seqtable
# Report_file: x13776.dan
########################################

#=======================================
#
# Sequence: X13776     from: 1   to: 2167
# HitCount: 2148
#=======================================

  Start     End  Strand     Tm     GC DeltaG DeltaH DeltaS TmProd Sequence
      1      20       +   64.9   70.0      .      .      .      . ggtaccgctggcc
gagcatc
      2      21       +   63.7   65.0      .      .      .      . gtaccgctggccg
agcatct
      3      22       +   63.7   65.0      .      .      .      . taccgctggccga
gcatctg
      4      23       +   66.9   70.0      .      .      .      . accgctggccgag
catctgc
      5      24       +   66.7   70.0      .      .      .      . ccgctggccgagc
atctgct
      6      25       +   65.5   70.0      .      .      .      . cgctggccgagca
tctgctc
      7      26       +   65.5   70.0      .      .      .      . gctggccgagcat
ctgctcg
      8      27       +   63.7   65.0      .      .      .      . ctggccgagcatc
tgctcga
      9      28       +   62.9   60.0      .      .      .      . tggccgagcatct
gctcgat
     10      29       +   62.6   65.0      .      .      .      . ggccgagcatctg
ctcgatc
     11      30       +   61.7   60.0      .      .      .      . gccgagcatctgc
tcgatca
     12      31       +   60.2   60.0      .      .      .      . ccgagcatctgct
cgatcac
     13      32       +   60.2   60.0      .      .      .      . cgagcatctgctc
gatcacc
     14      33       +   59.0   55.0      .      .      .      . gagcatctgctcg
atcacca
     15      34       +   59.2   55.0      .      .      .      . agcatctgctcga
tcaccac
     16      35       +   60.4   60.0      .      .      .      . gcatctgctcgat
caccacc
     17      36       +   58.9   55.0      .      .      .      . catctgctcgatc
accacca
     18      37       +   58.6   55.0      .      .      .      . atctgctcgatca
ccaccag
     19      38       +   61.3   60.0      .      .      .      . tctgctcgatcac
caccagc
     20      39       +   62.4   65.0      .      .      .      . ctgctcgatcacc
accagcc
     21      40       +   63.9   65.0      .      .      .      . tgctcgatcacca
ccagccg
     22      41       +   64.9   70.0      .      .      .      . gctcgatcaccac
cagccgg
     23      42       +   64.3   70.0      .      .      .      . ctcgatcaccacc
agccggg
     24      43       +   66.1   70.0      .      .      .      . tcgatcaccacca
gccgggc
     25      44       +   67.5   75.0      .      .      .      . cgatcaccaccag
ccgggcg
     26      45       +   66.1   70.0      .      .      .      . gatcaccaccagc
cgggcga
     27      46       +   66.3   70.0      .      .      .      . atcaccaccagcc
gggcgac
     28      47       +   68.6   75.0      .      .      .      . tcaccaccagccg
ggcgacg
     29      48       +   69.8   80.0      .      .      .      . caccaccagccgg
gcgacgg
     30      49       +   70.7   80.0      .      .      .      . accaccagccggg
cgacggg
     31      50       +   70.5   80.0      .      .      .      . ccaccagccgggc
gacggga
     32      51       +   68.6   75.0      .      .      .      . caccagccgggcg
acgggaa
     33      52       +   68.6   75.0      .      .      .      . accagccgggcga
cgggaac
     34      53       +   68.4   75.0      .      .      .      . ccagccgggcgac
gggaact


  [Part of this file has been deleted for brevity]

   2101    2120       +   69.9   80.0      .      .      .      . ggccggagcgctg
accctgc
   2102    2121       +   68.7   75.0      .      .      .      . gccggagcgctga
ccctgct
   2103    2122       +   65.5   70.0      .      .      .      . ccggagcgctgac
cctgcta
   2104    2123       +   63.5   65.0      .      .      .      . cggagcgctgacc
ctgctat
   2105    2124       +   61.3   60.0      .      .      .      . ggagcgctgaccc
tgctatt
   2106    2125       +   60.1   60.0      .      .      .      . gagcgctgaccct
gctattc
   2107    2126       +   61.7   60.0      .      .      .      . agcgctgaccctg
ctattcg
   2108    2127       +   63.4   65.0      .      .      .      . gcgctgaccctgc
tattcgc
   2109    2128       +   61.7   60.0      .      .      .      . cgctgaccctgct
attcgct
   2110    2129       +   59.5   55.0      .      .      .      . gctgaccctgcta
ttcgctt
   2111    2130       +   57.1   50.0      .      .      .      . ctgaccctgctat
tcgcttt
   2112    2131       +   56.4   45.0      .      .      .      . tgaccctgctatt
cgctttt
   2113    2132       +   54.7   45.0      .      .      .      . gaccctgctattc
gctttta
   2114    2133       +   55.0   45.0      .      .      .      . accctgctattcg
cttttac
   2115    2134       +   55.9   50.0      .      .      .      . ccctgctattcgc
ttttacc
   2116    2135       +   54.7   45.0      .      .      .      . cctgctattcgct
tttacct
   2117    2136       +   52.0   40.0      .      .      .      . ctgctattcgctt
ttaccta
   2118    2137       +   51.2   35.0      .      .      .      . tgctattcgcttt
tacctat
   2119    2138       +   50.9   40.0      .      .      .      . gctattcgctttt
acctatc
   2120    2139       +   49.0   35.0      .      .      .      . ctattcgctttta
cctatct
   2121    2140       +   49.3   35.0      .      .      .      . tattcgcttttac
ctatctg
   2122    2141       +   51.1   35.0      .      .      .      . attcgcttttacc
tatctgt
   2123    2142       +   52.2   40.0      .      .      .      . ttcgcttttacct
atctgtg
   2124    2143       +   54.0   45.0      .      .      .      . tcgcttttaccta
tctgtgg
   2125    2144       +   55.2   50.0      .      .      .      . cgcttttacctat
ctgtggg
   2126    2145       +   53.9   45.0      .      .      .      . gcttttacctatc
tgtgggt
   2127    2146       +   52.3   45.0      .      .      .      . cttttacctatct
gtgggtg
   2128    2147       +   53.5   45.0      .      .      .      . ttttacctatctg
tgggtgg
   2129    2148       +   56.0   50.0      .      .      .      . tttacctatctgt
gggtggc
   2130    2149       +   57.8   55.0      .      .      .      . ttacctatctgtg
ggtggcc
   2131    2150       +   60.1   60.0      .      .      .      . tacctatctgtgg
gtggccg
   2132    2151       +   63.4   65.0      .      .      .      . acctatctgtggg
tggccgc
   2133    2152       +   64.3   70.0      .      .      .      . cctatctgtgggt
ggccgcc
   2134    2153       +   63.4   65.0      .      .      .      . ctatctgtgggtg
gccgcca
   2135    2154       +   62.7   60.0      .      .      .      . tatctgtgggtgg
ccgccaa
   2136    2155       +   64.5   65.0      .      .      .      . atctgtgggtggc
cgccaac
   2137    2156       +   66.5   70.0      .      .      .      . tctgtgggtggcc
gccaacc
   2138    2157       +   66.8   70.0      .      .      .      . ctgtgggtggccg
ccaacca
   2139    2158       +   66.8   70.0      .      .      .      . tgtgggtggccgc
caaccag
   2140    2159       +   66.8   70.0      .      .      .      . gtgggtggccgcc
aaccagt
   2141    2160       +   65.9   65.0      .      .      .      . tgggtggccgcca
accagtt
   2142    2161       +   65.6   70.0      .      .      .      . gggtggccgccaa
ccagttc
   2143    2162       +   65.6   70.0      .      .      .      . ggtggccgccaac
cagttcc
   2144    2163       +   64.4   65.0      .      .      .      . gtggccgccaacc
agttcct
   2145    2164       +   64.1   65.0      .      .      .      . tggccgccaacca
gttcctc
   2146    2165       +   65.4   70.0      .      .      .      . ggccgccaaccag
ttcctcg
   2147    2166       +   64.2   65.0      .      .      .      . gccgccaaccagt
tcctcga
   2148    2167       +   62.4   65.0      .      .      .      . ccgccaaccagtt
cctcgag

#---------------------------------------
#---------------------------------------

  Output files for usage example 2

  Graphics File: dan.ps

   [dan results]

   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.

   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by the EMBOSS
   environment variable EMBOSS_DATA.

   To see the available EMBOSS data files, run:

% embossdata -showall

   To fetch one of the data files (for example 'Exxx.dat') into your
   current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

   Users can provide their own data files in their own directories.
   Project specific files can be put in the current directory, or for
   tidier directory listings in a subdirectory called ".embossdata".
   Files for all EMBOSS runs can be put in the user's home directory, or
   again in a subdirectory called ".embossdata".

   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata

Notes

   The enthalpy of a reaction equates to the "heat" of the reaction so
   long as temperate and pressure are constant. Enthalpy depends upon the
   strength of the chemical bonds and non-bonding interactions involved.
   The entropy of a reaction reflects the level of disorder or randomness
   of the molecules involved. The higher the entropy, the greater the
   disorder. The free energy of a reaction reflects it's ability to do
   work. It helps one determine whether a reaction is feasible given a
   set of conditions and it's quilibrium.

References

    1. 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.
    2. 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.

See also

   Program name                           Description
   banana       Plot bending and curvature data for B-DNA
   btwisted     Calculate the twisting in a B-DNA sequence
   chaos        Draw a chaos game representation plot for a nucleotide sequence
   compseq      Calculate the composition of unique words in sequences
   density      Draw a nucleic acid density plot
   freak        Generate residue/base frequency table or plot
   isochore     Plots isochores in DNA sequences
   sirna        Finds siRNA duplexes in mRNA
   wordcount    Count and extract unique words in DNA sequence(s)

Author(s)

   This program was originally included in EGCG under the names "MELT"
   and "MELTPLOT", written by Rodrigo Lopez (rls © ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   This application was written by Alan Bleasby (ajb © ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

History

   Written (1999) - Alan Bleasby

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
