ABOUT	SETUP	SEQUENCE	RULES	BOUQUET	OPTIONS	LEGAL
iDNA can support any type of "step" rule: di-, tri-, tetra-, or any number of nucleotides. For now, only the following di-nucleotide rules have been incorporated into the program. Name Source Bolshoy A. Bolshoy, P. McNamara, R.E. Harrington & E.N. Trifonov (1991) Proc. Natl. Acad. Sci. USA 88:2312-2316 (roll & tilt) W. Kabsch, C. Sanders & E.N. Trifonov (1982) Nucl. Acids Res. 10:1097-1104 (twist) De Santis P. De Santis, A. Palleschi, M. Savino & A. Scipioni (1990) Biochemistry 29:9269-9273 (twist, roll & tilt) Trifonov Trifonov, E.N. (1985) CRC Crit. Revs. Biochem. 19:89-106 (roll and tilt) Kabsch et al. 1982 (twist) Crystal The parameters are averaged from crystallographic structures (twist, roll & tilt) There is an optional setting to override the rules and to use a single set of helicoidals for all base steps regardless of base type.
Single Trajectory: enter a base sequence, select a helicoidal rule, leave the other settings alone and press the Execute button. Base Sequence Helicoidal Rule Bolshoy De Santis Trifonov Crystal Processing time increases with sequence length and the number of trajectories but it is much less than a minute if yours is the only request. It may take longer to get your results because of network delays. Multiple Trajectories: bouquets are generated only if the size is more than 1 and at least one standard deviation is greater than zero. Bouquet Size trajectories Standard Deviations Å rise | ° twist | ° roll | ° tilt Optional Settings: Leave the following at the preset values unless you really want different settings. Base Rise Å Use Single Helicoidals No, use the selected helicoidal rule Yes, use: ° twist | ° roll | ° tilt Rotation simultaneous sequential sequential: roll and tilt swapped simultaneous: roll and tilt swapped Remove Size Limits: Use of iDNA is free for up to 10000 trajectory-basepairs. To exceed this limit you have to pay US$1 per trajectory-basepair. All major credit cards accepted except Discover.

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