ABOUT
SETUP
SEQUENCE
RULES
BOUQUET
OPTIONS
LEGAL

Enter the base sequence using the single letter code: A, C, G, T in lower or upper case. No other letters of the alphabet are allowed. You can also enter multipliers and parentheses to group blocks of bases. You can also include spaces if that improves readability. For example, the following two lines are equivalent:

  1. acc((gtg)3 cct2)2 cc
  2. ACCGT GGTGG TGCCT TGTGG TGGTG CCTTC C

Interesting sequences (more to come). Copy a sequence and paste it into the sequence field of the form:

  1. ((cg)3A5(cg)3A4)7
  2. (g3c3(TAGAg4c3)2TAGA)4
  3. (gA4T4c)30

Sequences are limited to 1000 base pairs but note that you can enter only 300 characters in the sequence input box. To enter sequences longer than 300 characters you must use blocks and multipliers. Overlong sequences are truncated quietly. There must also be at least three bases. Obviously, multipliers are also limited to 1000.

For sequences of up to 300 base pairs, the sugar-phosphate backbones and a line connecting the backbones at each base pair will be shown. For longer sequences, only the helical axis will be drawn.

Cryptic error codes are returned if you make a mistake in entering the sequence. These codes are for the programmer and are no help to the user. If you use common sense in entering the sequence you should have no problem. Be careful using multipliers and especially when nesting blocks. The above example is as complicated as it should get.

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.

The Harvey Laboratory
Computer Lab
YammpWeb
Publications
Research
Teaching