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|
dan
Function
Calculates DNA RNA/DNA melting temperature
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
Here is a sample session with dan
% dan
Calculates DNA RNA/DNA 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 DNA RNA/DNA 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
-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 standard output
-filter boolean Read standard input, write 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: Sun 15 Jul 2007 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 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
#---------------------------------------
#---------------------------------------
Output files for usage example 2
Graphics File: dan.ps
[dan results]
File: x13776.dan
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
None.
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 Bending and curvature plot in B-DNA
btwisted Calculates the twisting in a B-DNA sequence
chaos Create a chaos game representation plot for a sequence
compseq Count composition of dimer/trimer/etc words in a sequence
freak Residue/base frequency table or plot
isochore Plots isochores in large DNA sequences
sirna Finds siRNA duplexes in mRNA
wordcount Counts words of a specified size in a DNA sequence
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
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