                                     dan



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   Please help by correcting and extending the Wiki pages.

Function

   Calculate 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, Baldino et al. Methods in Enzymol. 168,
   761-777, Allawi and SantaLucia (1997), Biochemistry 36:10581-10594).

Usage

   Here is a sample session with dan


% dan
Calculate 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
Calculate 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

Calculate nucleic acid melting temperature
Version: EMBOSS:6.6.0.0

   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,
                                  tek, tekt, none, data, xterm, png, gif, pdf,
                                  svg)
*  -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. (default -rformat seqtable)

   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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 and exit. 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
   -version            boolean    Report version number and exit


Input file format

   dan reads one or more nucleotide sequences.

   The input is a standard EMBOSS sequence query (also known as a 'USA').

   Major sequence database sources defined as standard in EMBOSS
   installations include srs:embl, srs:uniprot and ensembl

   Data can also be read from sequence output in any supported format
   written by an EMBOSS or third-party application.

   The input format can be specified by using the command-line qualifier
   -sformat xxx, where 'xxx' is replaced by the name of the required
   format. The available format names are: gff (gff3), gff2, embl (em),
   genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw),
   dasgff and debug.

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

  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 INSDC.
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 (amiR) of
RT   Pseudomonas 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 sequence 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 INSDC.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
XX
DR   GOA; Q51417.
DR   InterPro; IPR003211; AmiSUreI_transpt.
DR   UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE.


  [Part of this file has been deleted for brevity]

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 causes
FT                   constitutive expression of amiE"
FT   misc_difference 1281
FT                   /replace="g"
FT                   /note="conflict"
FT                   /citation=[3]
XX
SQ   Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other;
     ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat        60
     ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac       120
     aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg       180
     aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg       240
     agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc       300
     ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg       360
     tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg       420
     agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga       480
     acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga       540
     ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa       600
     gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct       660
     acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg       720
     cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg       780
     ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg       840
     aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt       900
     acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct       960
     tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc      1020
     tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt      1080
     acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca      1140
     gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc      1200
     agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt      1260
     ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg      1320
     cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca      1380
     gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt      1440
     gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc      1500
     gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc      1560
     cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga      1620
     tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa      1680
     gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca      1740
     ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct      1800
     gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg      1860
     aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt      1920
     catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg      1980
     gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct      2040
     gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa      2100
     ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt      2160
     cctcgag                                                                2167
//

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, dasgff, debug, listfile, dbmotif, diffseq,
   draw, restrict, excel, feattable, motif, nametable, 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.

   The output is to the specified graphics device.

   The results can be output in one of several formats by using the
   command-line qualifier -graph xxx, where 'xxx' is replaced by the name
   of the required device. Support depends on the availability of
   third-party software packages.

   The device names that output to a file are: ps (postscript), cps
   (colourps), png, gif, pdf, svg, hpgl, hp7470, hp7580, das, data.

   The other available device names are: meta, x11 (xwindows), tek
   (tek4107t), tekt (tektronix), xterm, text.

   Output can be turned off by specifying none (null).

   See: http://emboss.sf.net/docs/themes/GraphicsDevices.html for further
   information on supported devices.

   If the -plot qualifier is used, graphical output is produced instead.

  Output files for usage example

  File: x13776.dan

########################################
# Program: dan
# Rundate: Mon 15 Jul 2013 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      .      .      .      . ggtaccgctggccg
agcatc
      2      21       +   63.7   65.0      .      .      .      . gtaccgctggccga
gcatct
      3      22       +   63.7   65.0      .      .      .      . taccgctggccgag
catctg
      4      23       +   66.9   70.0      .      .      .      . accgctggccgagc
atctgc
      5      24       +   66.7   70.0      .      .      .      . ccgctggccgagca
tctgct
      6      25       +   65.5   70.0      .      .      .      . cgctggccgagcat
ctgctc
      7      26       +   65.5   70.0      .      .      .      . gctggccgagcatc
tgctcg
      8      27       +   63.7   65.0      .      .      .      . ctggccgagcatct
gctcga
      9      28       +   62.9   60.0      .      .      .      . tggccgagcatctg
ctcgat
     10      29       +   62.6   65.0      .      .      .      . ggccgagcatctgc
tcgatc
     11      30       +   61.7   60.0      .      .      .      . gccgagcatctgct
cgatca
     12      31       +   60.2   60.0      .      .      .      . ccgagcatctgctc
gatcac
     13      32       +   60.2   60.0      .      .      .      . cgagcatctgctcg
atcacc
     14      33       +   59.0   55.0      .      .      .      . gagcatctgctcga
tcacca
     15      34       +   59.2   55.0      .      .      .      . agcatctgctcgat
caccac
     16      35       +   60.4   60.0      .      .      .      . gcatctgctcgatc
accacc
     17      36       +   58.9   55.0      .      .      .      . catctgctcgatca
ccacca
     18      37       +   58.6   55.0      .      .      .      . atctgctcgatcac
caccag
     19      38       +   61.3   60.0      .      .      .      . tctgctcgatcacc
accagc
     20      39       +   62.4   65.0      .      .      .      . ctgctcgatcacca
ccagcc
     21      40       +   63.9   65.0      .      .      .      . tgctcgatcaccac
cagccg
     22      41       +   64.9   70.0      .      .      .      . gctcgatcaccacc
agccgg
     23      42       +   64.3   70.0      .      .      .      . ctcgatcaccacca
gccggg
     24      43       +   66.1   70.0      .      .      .      . tcgatcaccaccag
ccgggc
     25      44       +   67.5   75.0      .      .      .      . cgatcaccaccagc
cgggcg
     26      45       +   66.1   70.0      .      .      .      . gatcaccaccagcc
gggcga
     27      46       +   66.3   70.0      .      .      .      . atcaccaccagccg
ggcgac
     28      47       +   68.6   75.0      .      .      .      . tcaccaccagccgg
gcgacg
     29      48       +   69.8   80.0      .      .      .      . caccaccagccggg
cgacgg
     30      49       +   70.7   80.0      .      .      .      . accaccagccgggc
gacggg
     31      50       +   70.5   80.0      .      .      .      . ccaccagccgggcg
acggga
     32      51       +   68.6   75.0      .      .      .      . caccagccgggcga
cgggaa
     33      52       +   68.6   75.0      .      .      .      . accagccgggcgac
gggaac
     34      53       +   68.4   75.0      .      .      .      . ccagccgggcgacg
ggaact


  [Part of this file has been deleted for brevity]

   2101    2120       +   69.9   80.0      .      .      .      . ggccggagcgctga
ccctgc
   2102    2121       +   68.7   75.0      .      .      .      . gccggagcgctgac
cctgct
   2103    2122       +   65.5   70.0      .      .      .      . ccggagcgctgacc
ctgcta
   2104    2123       +   63.5   65.0      .      .      .      . cggagcgctgaccc
tgctat
   2105    2124       +   61.3   60.0      .      .      .      . ggagcgctgaccct
gctatt
   2106    2125       +   60.1   60.0      .      .      .      . gagcgctgaccctg
ctattc
   2107    2126       +   61.7   60.0      .      .      .      . agcgctgaccctgc
tattcg
   2108    2127       +   63.4   65.0      .      .      .      . gcgctgaccctgct
attcgc
   2109    2128       +   61.7   60.0      .      .      .      . cgctgaccctgcta
ttcgct
   2110    2129       +   59.5   55.0      .      .      .      . gctgaccctgctat
tcgctt
   2111    2130       +   57.1   50.0      .      .      .      . ctgaccctgctatt
cgcttt
   2112    2131       +   56.4   45.0      .      .      .      . tgaccctgctattc
gctttt
   2113    2132       +   54.7   45.0      .      .      .      . gaccctgctattcg
ctttta
   2114    2133       +   55.0   45.0      .      .      .      . accctgctattcgc
ttttac
   2115    2134       +   55.9   50.0      .      .      .      . ccctgctattcgct
tttacc
   2116    2135       +   54.7   45.0      .      .      .      . cctgctattcgctt
ttacct
   2117    2136       +   52.0   40.0      .      .      .      . ctgctattcgcttt
taccta
   2118    2137       +   51.2   35.0      .      .      .      . tgctattcgctttt
acctat
   2119    2138       +   50.9   40.0      .      .      .      . gctattcgctttta
cctatc
   2120    2139       +   49.0   35.0      .      .      .      . ctattcgcttttac
ctatct
   2121    2140       +   49.3   35.0      .      .      .      . tattcgcttttacc
tatctg
   2122    2141       +   51.1   35.0      .      .      .      . attcgcttttacct
atctgt
   2123    2142       +   52.2   40.0      .      .      .      . ttcgcttttaccta
tctgtg
   2124    2143       +   54.0   45.0      .      .      .      . tcgcttttacctat
ctgtgg
   2125    2144       +   55.2   50.0      .      .      .      . cgcttttacctatc
tgtggg
   2126    2145       +   53.9   45.0      .      .      .      . gcttttacctatct
gtgggt
   2127    2146       +   52.3   45.0      .      .      .      . cttttacctatctg
tgggtg
   2128    2147       +   53.5   45.0      .      .      .      . ttttacctatctgt
gggtgg
   2129    2148       +   56.0   50.0      .      .      .      . tttacctatctgtg
ggtggc
   2130    2149       +   57.8   55.0      .      .      .      . ttacctatctgtgg
gtggcc
   2131    2150       +   60.1   60.0      .      .      .      . tacctatctgtggg
tggccg
   2132    2151       +   63.4   65.0      .      .      .      . acctatctgtgggt
ggccgc
   2133    2152       +   64.3   70.0      .      .      .      . cctatctgtgggtg
gccgcc
   2134    2153       +   63.4   65.0      .      .      .      . ctatctgtgggtgg
ccgcca
   2135    2154       +   62.7   60.0      .      .      .      . tatctgtgggtggc
cgccaa
   2136    2155       +   64.5   65.0      .      .      .      . atctgtgggtggcc
gccaac
   2137    2156       +   66.5   70.0      .      .      .      . tctgtgggtggccg
ccaacc
   2138    2157       +   66.8   70.0      .      .      .      . ctgtgggtggccgc
caacca
   2139    2158       +   66.8   70.0      .      .      .      . tgtgggtggccgcc
aaccag
   2140    2159       +   66.8   70.0      .      .      .      . gtgggtggccgcca
accagt
   2141    2160       +   65.9   65.0      .      .      .      . tgggtggccgccaa
ccagtt
   2142    2161       +   65.6   70.0      .      .      .      . gggtggccgccaac
cagttc
   2143    2162       +   65.6   70.0      .      .      .      . ggtggccgccaacc
agttcc
   2144    2163       +   64.4   65.0      .      .      .      . gtggccgccaacca
gttcct
   2145    2164       +   64.1   65.0      .      .      .      . tggccgccaaccag
ttcctc
   2146    2165       +   65.4   70.0      .      .      .      . ggccgccaaccagt
tcctcg
   2147    2166       +   64.2   65.0      .      .      .      . gccgccaaccagtt
cctcga
   2148    2167       +   62.4   65.0      .      .      .      . ccgccaaccagttc
ctcgag

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

  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.
    3. Allawi H.T. and SantaLucia J. Jr. (1997), "Thermodynamics and NMR
       of Internal G*T Mismatches in DNA" Biochemistry 36, 10581-10594.

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     Plot isochores in DNA sequences
                    wordcount    Count and extract unique words in molecular sequence(s)

Author(s)

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

                    Please report all bugs to the EMBOSS bug team
                    (emboss-bug (c) emboss.open-bio.org) not to the original author.

                    This application was written by Alan Bleasby
   European         Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton,         Cambridge CB10 1SD, UK

                    Please report all bugs to the EMBOSS bug team
                    (emboss-bug (c) emboss.open-bio.org) not to the original author.

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
