PDraw32 is a freeware DNA sequence analysis program for Windows platforms written by Kjeld Olesen and available at Acaclone.com (http://www.acaclone.com/).

• Drawing of circular or linear DNA maps with user-entered features marked.
• An unusual and interesting display of G+C distribution.
• Search and labeling of restriction sites. Also gives tabular output of site coordinates and fragment sizes.
• Sequence editing and manipulation.
• ORF marking (based on size).
• Oligo Tm calculation including correction for primer concentration, salt, and solvents.
• Dot plot between two sequences.

• Upgrades are promised.  These notes were made on revision 1.1.86.
• There is little documentation.  The interface is relatively intuitive, but caution is required to avoid being misled.
• The input format is not defined, but can be deduced by loading a sequence as plain text and then saving it.  Apparently there is a fixed format header that saves parameters of the pdraw session followed by a ".."  Thereafter characters are interpreted as DNA sequence with numbers spaces and letters not in the 16 character ambiguity set for DNA being ignored.  It will take a plain text file after complaining about the missing " ..".  If you try to load a fasta file, it will incorporate letters from the header into the sequence.  The same will happen for an html file.  Hence be sure to verify the length, beginning, and ending of a sequence after loading.
• It appears to use the standard DNA ambiguity codes. Do not attempt to load protein sequences.  If your sequence has ambiguity codes, be careful to run controls to see how they are used.  For example, the sequence GANTTC was not recognized as an EcoRI site.
• The restriction analysis appears to handle large sequences well as advertised at the acaclone page.
• The restrictions enzymes definition file installs in \program files\pDRAW32\ENZYMES.DAT.  The format is not defined, and does not appear to correspond to a REBASE format.  So it is unclear how to update the list of available enzymes, except perhaps by reinstalling the program.  You could try hand editing the file to include some new enzyme of interest.  The meanings of most of the fields are apparent.  The field with the string of letters contains codes for suppliers, which you could leave as blank.  The 3rd and 4th numeric fields are the cut site relative to the start, and the offset from the cut site to the cut site on the complementary strand.  The first two numeric fields are true/false flags of unknown meaning.  It appears that more than one record by the same name can be entered to handle sites that can not be encoded by a single record using ambiguity codes.  e.g., see CspCI.
• The block size for %GC coloring appears to be computed as a variable from the length of the input sequence.  It is not obvious if there is a way to override this.  Short sequences are plotted as 1 base blocks, but in some cases the results make no sense with respect to the actual sequence eg. try GAATTC.  Hence there are bugs in the routine, so be sure to verify any conclusion you might draw from viewing the %GC presentation.
• For oligo analysis, there are corrections for primer concentration, salt, and solvent conditions set up under <settings> <analysis setup>.
• The Tm calculator under <utilities> uses the parameter settings in force when the calculator window is opened.  To change the conditions, first close the calculator window, change them under <settings>, and then reopen the calculator window and reenter the oligo sequence.
• If an oligo sequence that matches the loaded template is added to the oligo database under <utilities>, and selected under <analysis>, then when analysis is conducted a report will appear under <view>
• AWAITING BENCHMARK VS. OLIGO PROGRAM.
• The dot plotter (under <utilities> works by clicking on its setup tab to define the plot, then clicking on the plot tab to execute and see the result.
• The start and stop entries on the setup tab appear not to function???  To analyze only part of a sequence, you would apparently have to make files having only those parts.
• To make a dot requires perfect matching over the length defined by window.  If I interpret the step length literally, then it should be set equal to or smaller than the window to avoid skipping over sequences altoghether.  It is hard for me to see a reason not to use 1 for step length, unless the sequence is large and execution is just slow.
• Both read and blue dots are produced.  The red dots are complementary matches.  A red and blue dot at the same position plot as a red dot.
• The "size relative" parameter scales the plot down if you enter a size greater than the sequence length.  It does nothing if you enter a size smaller than the sequence length.
• Ambiguity codes are not interpreted as such but instead matched literally.  You still can't dot plot a protein sequence, however, because upon loading it will have residues deleted that do not correspond to legal DNA ambiguity codes.