Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases

dan calculates the melting temperature (Tm) and the percent G+C of a nucleic acid sequence (optionally plotting them).

Here is a sample session with dan:

% dan Input sequence: embl:paamir Enter window size [20]: Enter Shift Increment [1]: Enter DNA concentration (nM) [50.]: Enter salt concentration (mM) [50.]: Output file [paamir.dan]:

An example of producing a plot of Tm:

% dan -plot Input sequence(s): embl:paamir Enter window size [20]: Enter Shift Increment [1]: Enter DNA concentration (nM) [50.]: Enter salt concentration (mM) [50.]: Enter minimum temperature [55.]: Graph type [x11]:

Mandatory qualifiers (bold if not always prompted):

[-sequence] (seqall)

Sequence database USA.

-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, and the properties are calculated at each new position.

-shiftincrement (integer)

This is the amount the window is moved at each increment in order to find the melting point and other properties along the sequence.

-dnaconc (float)

Enter DNA concentration (nM).

-saltconc (float)

Enter salt concentration (mM).

-formamide (float)

This specifies the percent formamide to be used in calculations (ignored unless-product is used).

-mismatch (float)

This specifies the percent mismatch to be used in calculations (ignored unless-product is used).

-prodlen (integer)

This specifies the product length to be used in calculations (ignored unless-product is used).

-mintemp (float)

Enter a minimum value for the temperature scale (y-axis) of the plot.

-graph (xygraph)

Graph type.

-outfile (report)

If a plot is not being produced, data (on the melting point etc., in each window along the sequence) is output to this file.

Optional qualifiers (bold if not always prompted):

-temperature (float)

If -thermo has been specified, this specifies the temperature at which to calculate the DeltaG, DeltaH and DeltaS values.

Advanced qualifiers:

-rna (boolean)

This specifies that the sequence is an RNA sequence, not a DNA sequence.

-product (boolean)

This prompts for percent formamide, percent of mismatches allowed, and product length.

-thermo (boolean)

Output the DeltaG, DeltaH, and DeltaS values of the sequence windows to the output data file.

-plot (boolean)

If this is not specified, the file of output data is produced, else a plot of the melting point along the sequence is produced.