First try out the program with this example input-file for
a DNA octamer with a single point mutation leading to an A:T basepair "moving"
through the sequence (8 spots and 8 target strands). Note that in this file the
only example input file that contains explanatory comments.
This is a second example input file for DNA 65-mers as probes and targets (20 spots and 15 target strands).
A third, bigger example for DNA octamers (100 spots and 42 target strands).
Note that the data file has to be in the specific format demonstrated in the example files above. It currently has to be ASCII text, as obtained, for example, with the "notepad" editor of Windows 2000 or simple text editors on other platforms. Formatted text from e.g. Word or other applications will not be accepted, though a Word document created in the correct format and saved as "text only with line breaks" will be accepted from Windows and all common Unices (but not Mac - as the Mac uses a different Character to seperate lines ) platforms. Please note that incomplete or error-containing data matrices will necessarily lead to output errors.
It is recommended that you save one of the example files to your PC (Fils->Save page as...). You can then edit the file to contain your own data. For other sequences than those provided, you will have to calculate free energies of duplex formation, e.g. using HyTher (by Drs. Peyret and SantaLucia, Wayne State University) or MELTING (by Dr. Le Novere, Pasteur Institute) or Mfold (Dr. Zuker, Rensselaer Polytechnic Institute).
Check the results you recieve from these programs! HyTher for example seems to print 0 for "no hybridization at all". This should be replaced by some negative value.
Please save your edited data
file as an ASCII text, as mentioned above, and then upload it from your PC,
using the "Browse" button provided below. Then press "Submit Query" after
choosing one of the Output options. It is recommended that you work down
the list of Output options to ensure that the results obtained are reasonable.