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DAN : Calculates DNA RNA/DNA melting temperature (EMBOSS)



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( = required, = conditionally required)


input Section


required Section


advanced Section


output Section


input Section


sequence -- DNA [sequences] (-sequence) : please enter
either :
  1. the name of a file:
  2. or the actual data here:

(sequence format)


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required Section

Enter window size (-windowsize)
Enter Shift Increment (-shiftincrement)
Enter DNA concentration (nM) (-dnaconc)
Enter salt concentration (mM) (-saltconc)

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advanced Section

Use RNA data values (-rna)

productsection Section


thermosection Section


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productsection Section

Prompt for product values (-product)
Enter percentage of formamide (-formamide)
Enter percent mismatch (-mismatch)
Enter the product length (-prodlen)

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thermosection Section

Thermodynamic calculations (-thermo)
Enter temperature (-temperature)

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output Section

Produce a plot (-plot)
Enter minimum temperature (-mintemp)

graph (-graph)
Output data file (-outfile)

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Some explanations about the options


thermosection Section
Thermodynamic calculations (-thermo)
Output the DeltaG, DeltaH and DeltaS values of the sequence windows to the output data file.
Enter temperature (-temperature)
If -thermo has been specified then this specifies the temperature at which to calculate the DeltaG, DeltaH and DeltaS values.

input Section
enter either the name of a file or the actual data
if you are using Netscape 2.x or later, you can select a file by typing its name, or better, by selecting it with the Netscape file browser (Browse button)
OR you can type your data in the next area, or cut and paste it from another application.
(but not both)

advanced Section
Use RNA data values (-rna)
This specifies that the sequence is an RNA sequnce and not a DNA sequence.

required Section
Enter window size (-windowsize)
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 calcualted at each new position.
Enter Shift Increment (-shiftincrement)
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.

output Section
Produce a plot (-plot)
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.
Enter minimum temperature (-mintemp)
Enter a minimum value for the temperature scale (y-axis) of the plot.
Output data file (-outfile)
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.

productsection Section
Prompt for product values (-product)
This prompts for percent formamide, percent of mismatches allowed and product length.
Enter percentage of formamide (-formamide)
This specifies the percent formamide to be used in calculations (it is ignored unless -product is used).
Enter percent mismatch (-mismatch)
This specifies the percent mismatch to be used in calculations (it is ignored unless -product is used).
Enter the product length (-prodlen)
This specifies the product length to be used in calculations (it is ignored unless -product is used).
Sequence format
The sequence will be automatically converted in the format needed for the program
providing you enter a sequence either:
in plain (raw) sequence format or in one of the following known formats:
IG,GenBank,NBRF,EMBL,GCG,DNAStrider,Fitch,fasta,Phylip,PIR,MSF,ASN,PAUP,CLUSTALW
You may enter in the text area a database entry code, or an accession number, in this form:
database:entry_name
or:
database:accession.

Pise form generator version: 5.a (16 Dec 2002 11:53)