How to Create and Edit an RNA or DNA Sequence

For a new sequence, select "File -> New Sequence" from the menu. This brings up an empty sequence editor window. Type a title into the title box, if desired. Then, click the comment box with your mouse. Here, you may type a comment of any number of lines, if you wish. Finally, move to the sequence box and type in your sequence 5' to 3'. You may use T's, U's, or both. The RNA folding algorithm assumes the sequence is RNA and will interpret a T as a U. The DNA folding module will likewise assume DNA and interpret U as T.

You may also use X to represent a gap or unknown base. Before exiting, select "File -> Save Sequence" or "File -> Save Sequence As..." to save the sequence. Sequences can be saved in SEQ or FASTA formats.

WARNING: Bases entered in lower case are not allowed to base pair in any generated structure, so make sure to enter all bases in UPPER-CASE unless you intentionally want to mark them as unpaired.  For example, in the sequence ACCGGAuucaGAUAG, the blue lower-case bases will not be allowed to base pair.

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Loading Sequences

To load a sequence, select "File -> Open Sequence." Three types of files can be loaded: sequence (SEQ) files, Genbank files, and simple text files. Sequence files follow a specific sequence format (See "Appendix A: File Formats"), Genbank files follow the Genbank format, and simple text files contain a sequence of bases with nothing else.

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Editor Features

For ease of entering a sequence, the RNAstructure editor can give audio feedback as a sequence is entered. If your computer has sound capabilities, there are two different ways by which a structure can be read out loud. If the "Speak While Typing" checkbox under the "Speak" menu is selected, bases will be read out loud as they are typed into the editor. and the "Speak While Typing" checkbox is selected, you will hear the sequence being read as it is typed into the editor. If the "Speak Sequence" menu item is clicked, the sequence will be read aloud from the beginning in its entirety. The "Stop Speaking" button will stop this automatic reading at any time. When the "Speak Sequence" button is pressed again, reading restarts at the beginning of the sequence.

The editor can format a sequence into a Genbank-like format. Pressing the "Format" button will arrange the sequence into segments 10 bases long, separated by spaces, with a maximum of five segments (50 bases) per line.

The "Fold RNA" and "Fold DNA" buttons will input the sequence directly into the "Fold" module, with the appropriate nucleic acid type selected. RNAstructure will request that the sequence be saved as a sequence file first, if the sequence has not been saved.