AveRNA input:

Sequence:
A string containing the letters A, C, G, U, or T, representing the bases Adenine, Cytosine, Guanine, Uracil, and Thymine, respectively. Lower case letters (a, c, g, u, or t) are accepted. Spaces may be inserted between the characters and will be removed when the calculation is performed. The left end of the sequence corresponds to the 5' end of the strand. To keep the load on our server manageable and response times reasonably low, we limit the length of AveRNA's inputs to 500 nucleotides (for longer sequences download the software from the project page).

Base-pair threshold:
The base-pair probability threshold times 100. See the manuscript for more details.

Get results ...:
The user can choose whether to view the output on a dynamically generated web page, or to receive the output via email, or both, by clicking one or both of the "as web page" and "via e-mail" boxes. If a computation takes more than 1 minute, the web interface notifies the user that the result will be sent out only via e-mail. The user must enter an email address in the box provided, in order to get the output via email.

Output structure:

AveRNA returns the consensus secondary structure in dot-parentheses format in which a matching pair of parentheses/brackets/braces denotes a base pair and a dot denotes an unpaired base. The structure is presented below the corresponding pair of strands, and the structure symbols are aligned with the corresponding base in the strand. The structure can be visualized by using the Pseudoviewer web page or software.

Individual predictions:
The predicted structures obtained from each of the individual algorithms.

Base-pair probabilities:
AveRNA returns the base-pair probabilities as comma separated values (CSV) files. Entitiy (i, j) corresponds to the probability of sequence positions i and j forming a base-pair.

Query ID:
Identifier of the query - this is primarily used for maintainance and debugging purposes.

Send these results by e-mail to ...:
Allows the user to send out the results via e-mail (primarily to themselves). Specify only one e-mail address in the field and press the "Send" button to send out the e-mail version of the results webpage.