Dotplot service request form

This Dot Plot can be used to find regions of complementary sequence (hence potential stable intermolecular base pairing) in two different single stranded RNA or DNA molcecules (self-complementarity and consequently intramolecular base pairing should be investigated using the 'Tinoco' dot plot tool here).
Given two RNA or RNA sequences, this tool will calculate all possible helices and display them in a two dimensional plot. Choosing 'DNA' only Watson-Crick base pairing is allowed whereas 'RNA' performs also G:U base pairing. The parameter 'minimum helix length' is used to suppress the display of smaller helices.

The output formats are PDF, PostScript, CSV, and GIF. PDF can be displayed by Adobe's Acrobat Reader, PostScript has also to be displayed by an external viewer (Ghostscript), CSV is viewable in a spreadsheet program, and GIF is automatically embedded in a HTML document as 'inline image'. GIF output is currently limited to sequences shorter than 200 Nts in length.

Sequence title: (plain format without spacing) [optional]

Sequence 1: (Format: plain text; no numbers; length < 3000 nts) [required]

Sequence 2: (Format: plain text; no numbers; length < 3000 nts) [required]

Nucleic acid type: ('RNA': also G:U base pairing allowed)
Minimum helix length: (smaller helices are suppressed)
Output format:

And now: or the form to defaults.

If you have any suggestions or comments on this service, just send us a mail.
M. Schmitz & S. Gräf
Last modified: Wed Jun 13 10:34:30 CEST 2001