dan

## Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

## 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, 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 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]: ```

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 ```

## Command line arguments

 ```Calculates nucleic acid melting temperature Version: EMBOSS:6.4.0.0 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 -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 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 ```

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-sequence]
(Parameter 1)
seqall Nucleotide sequence(s) filename and optional format, or reference (input USA) Readable sequence(s) Required
-windowsize integer 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 20
-shiftincrement integer 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 1
-dnaconc float Enter DNA concentration (nM) Number from 1.000 to 100000.000 50.
-saltconc float Enter salt concentration (mM) Number from 1.000 to 1000.000 50.
-mintemp float Enter a minimum value for the temperature scale (y-axis) of the plot. Number from 0.000 to 150.000 55.
-graph xygraph Graph type EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg EMBOSS_GRAPHICS value, or x11
-outfile report 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) <*>.dan
-product toggle This prompts for percent formamide, percent of mismatches allowed and product length. Toggle value Yes/No No
-formamide float This specifies the percent formamide to be used in calculations (it is ignored unless -product is used). Number from 0.000 to 100.000 0.
-mismatch float This specifies the percent mismatch to be used in calculations (it is ignored unless -product is used). Number from 0.000 to 100.000 0.
-prodlen integer This specifies the product length to be used in calculations (it is ignored unless -product is used). Any integer value Window size (20)
-thermo toggle Output the DeltaG, DeltaH and DeltaS values of the sequence windows to the output data file. Toggle value Yes/No No
-temperature float 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 25.
-rna boolean This specifies that the sequence is an RNA sequence and not a DNA sequence. Boolean value Yes/No No
-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. Toggle value Yes/No No
Associated qualifiers
"-sequence" associated seqall qualifiers
-sbegin1
-sbegin_sequence
integer Start of each sequence to be used Any integer value 0
-send1
-send_sequence
integer End of each sequence to be used Any integer value 0
-sreverse1
-sreverse_sequence
boolean Reverse (if DNA) Boolean value Yes/No N
boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide1
-snucleotide_sequence
boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein1
-sprotein_sequence
boolean Sequence is protein Boolean value Yes/No N
-slower1
-slower_sequence
boolean Make lower case Boolean value Yes/No N
-supper1
-supper_sequence
boolean Make upper case Boolean value Yes/No N
-sformat1
-sformat_sequence
string Input sequence format Any string
-sdbname1
-sdbname_sequence
string Database name Any string
-sid1
-sid_sequence
string Entryname Any string
-ufo1
-ufo_sequence
string UFO features Any string
-fformat1
-fformat_sequence
string Features format Any string
-fopenfile1
-fopenfile_sequence
string Features file name Any string
"-graph" associated xygraph qualifiers
-gprompt boolean Graph prompting Boolean value Yes/No N
-gdesc string Graph description Any string DNA melting plot
-gtitle string Graph title Any string
-gsubtitle string Graph subtitle Any string
-gxtitle string Graph x axis title Any string
-gytitle string Graph y axis title Any string
-goutfile string Output file for non interactive displays Any string
-gdirectory string Output directory Any string
"-outfile" associated report qualifiers
-rformat string Report format Any string seqtable
-rname string Base file name Any string
-rextension string File name extension Any string
-rdirectory string Output directory Any string
-raccshow boolean Show accession number in the report Boolean value Yes/No N
-rdesshow boolean Show description in the report Boolean value Yes/No N
-rscoreshow boolean Show the score in the report Boolean value Yes/No Y
-rstrandshow boolean Show the nucleotide strand in the report Boolean value Yes/No Y
-rusashow boolean Show the full USA in the report Boolean value Yes/No N
-rmaxall integer Maximum total hits to report Any integer value 0
-rmaxseq integer Maximum hits to report for one sequence Any integer value 0
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

## 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 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 (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 EMBL/GenBank/DDBJ databases. 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 /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 causes 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 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.

### File: x13776.dan

 ```######################################## # Program: dan # Rundate: Fri 15 Jul 2011 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 . . . . ggtaccgctggccgagcatc 2 21 + 63.7 65.0 . . . . gtaccgctggccgagcatct 3 22 + 63.7 65.0 . . . . taccgctggccgagcatctg 4 23 + 66.9 70.0 . . . . accgctggccgagcatctgc 5 24 + 66.7 70.0 . . . . ccgctggccgagcatctgct 6 25 + 65.5 70.0 . . . . cgctggccgagcatctgctc 7 26 + 65.5 70.0 . . . . gctggccgagcatctgctcg 8 27 + 63.7 65.0 . . . . ctggccgagcatctgctcga 9 28 + 62.9 60.0 . . . . tggccgagcatctgctcgat 10 29 + 62.6 65.0 . . . . ggccgagcatctgctcgatc 11 30 + 61.7 60.0 . . . . gccgagcatctgctcgatca 12 31 + 60.2 60.0 . . . . ccgagcatctgctcgatcac 13 32 + 60.2 60.0 . . . . cgagcatctgctcgatcacc 14 33 + 59.0 55.0 . . . . gagcatctgctcgatcacca 15 34 + 59.2 55.0 . . . . agcatctgctcgatcaccac 16 35 + 60.4 60.0 . . . . gcatctgctcgatcaccacc 17 36 + 58.9 55.0 . . . . catctgctcgatcaccacca 18 37 + 58.6 55.0 . . . . atctgctcgatcaccaccag 19 38 + 61.3 60.0 . . . . tctgctcgatcaccaccagc 20 39 + 62.4 65.0 . . . . ctgctcgatcaccaccagcc 21 40 + 63.9 65.0 . . . . tgctcgatcaccaccagccg 22 41 + 64.9 70.0 . . . . gctcgatcaccaccagccgg 23 42 + 64.3 70.0 . . . . ctcgatcaccaccagccggg 24 43 + 66.1 70.0 . . . . tcgatcaccaccagccgggc 25 44 + 67.5 75.0 . . . . cgatcaccaccagccgggcg 26 45 + 66.1 70.0 . . . . gatcaccaccagccgggcga 27 46 + 66.3 70.0 . . . . atcaccaccagccgggcgac 28 47 + 68.6 75.0 . . . . tcaccaccagccgggcgacg 29 48 + 69.8 80.0 . . . . caccaccagccgggcgacgg 30 49 + 70.7 80.0 . . . . accaccagccgggcgacggg 31 50 + 70.5 80.0 . . . . ccaccagccgggcgacggga 32 51 + 68.6 75.0 . . . . caccagccgggcgacgggaa 33 52 + 68.6 75.0 . . . . accagccgggcgacgggaac 34 53 + 68.4 75.0 . . . . ccagccgggcgacgggaact [Part of this file has been deleted for brevity] 2101 2120 + 69.9 80.0 . . . . ggccggagcgctgaccctgc 2102 2121 + 68.7 75.0 . . . . gccggagcgctgaccctgct 2103 2122 + 65.5 70.0 . . . . ccggagcgctgaccctgcta 2104 2123 + 63.5 65.0 . . . . cggagcgctgaccctgctat 2105 2124 + 61.3 60.0 . . . . ggagcgctgaccctgctatt 2106 2125 + 60.1 60.0 . . . . gagcgctgaccctgctattc 2107 2126 + 61.7 60.0 . . . . agcgctgaccctgctattcg 2108 2127 + 63.4 65.0 . . . . gcgctgaccctgctattcgc 2109 2128 + 61.7 60.0 . . . . cgctgaccctgctattcgct 2110 2129 + 59.5 55.0 . . . . gctgaccctgctattcgctt 2111 2130 + 57.1 50.0 . . . . ctgaccctgctattcgcttt 2112 2131 + 56.4 45.0 . . . . tgaccctgctattcgctttt 2113 2132 + 54.7 45.0 . . . . gaccctgctattcgctttta 2114 2133 + 55.0 45.0 . . . . accctgctattcgcttttac 2115 2134 + 55.9 50.0 . . . . ccctgctattcgcttttacc 2116 2135 + 54.7 45.0 . . . . cctgctattcgcttttacct 2117 2136 + 52.0 40.0 . . . . ctgctattcgcttttaccta 2118 2137 + 51.2 35.0 . . . . tgctattcgcttttacctat 2119 2138 + 50.9 40.0 . . . . gctattcgcttttacctatc 2120 2139 + 49.0 35.0 . . . . ctattcgcttttacctatct 2121 2140 + 49.3 35.0 . . . . tattcgcttttacctatctg 2122 2141 + 51.1 35.0 . . . . attcgcttttacctatctgt 2123 2142 + 52.2 40.0 . . . . ttcgcttttacctatctgtg 2124 2143 + 54.0 45.0 . . . . tcgcttttacctatctgtgg 2125 2144 + 55.2 50.0 . . . . cgcttttacctatctgtggg 2126 2145 + 53.9 45.0 . . . . gcttttacctatctgtgggt 2127 2146 + 52.3 45.0 . . . . cttttacctatctgtgggtg 2128 2147 + 53.5 45.0 . . . . ttttacctatctgtgggtgg 2129 2148 + 56.0 50.0 . . . . tttacctatctgtgggtggc 2130 2149 + 57.8 55.0 . . . . ttacctatctgtgggtggcc 2131 2150 + 60.1 60.0 . . . . tacctatctgtgggtggccg 2132 2151 + 63.4 65.0 . . . . acctatctgtgggtggccgc 2133 2152 + 64.3 70.0 . . . . cctatctgtgggtggccgcc 2134 2153 + 63.4 65.0 . . . . ctatctgtgggtggccgcca 2135 2154 + 62.7 60.0 . . . . tatctgtgggtggccgccaa 2136 2155 + 64.5 65.0 . . . . atctgtgggtggccgccaac 2137 2156 + 66.5 70.0 . . . . tctgtgggtggccgccaacc 2138 2157 + 66.8 70.0 . . . . ctgtgggtggccgccaacca 2139 2158 + 66.8 70.0 . . . . tgtgggtggccgccaaccag 2140 2159 + 66.8 70.0 . . . . gtgggtggccgccaaccagt 2141 2160 + 65.9 65.0 . . . . tgggtggccgccaaccagtt 2142 2161 + 65.6 70.0 . . . . gggtggccgccaaccagttc 2143 2162 + 65.6 70.0 . . . . ggtggccgccaaccagttcc 2144 2163 + 64.4 65.0 . . . . gtggccgccaaccagttcct 2145 2164 + 64.1 65.0 . . . . tggccgccaaccagttcctc 2146 2165 + 65.4 70.0 . . . . ggccgccaaccagttcctcg 2147 2166 + 64.2 65.0 . . . . gccgccaaccagttcctcga 2148 2167 + 62.4 65.0 . . . . ccgccaaccagttcctcgag #--------------------------------------- #--------------------------------------- ```

### Graphics File: dan.ps

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:

• .embossdata (under your current 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.

None.

0 if successful.

## Known bugs

None.

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
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 © 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 © 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.