PairFold input:

Sequence 1 and Sequence 2:
Each of the first and second sequences must be 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 PairFold's inputs to 500.

Sequence type:
By selecting the desired choice (RNA or DNA), the user specifies whether the strands should be folded using RNA parameters or DNA parameters. RNA is the default. If RNA is chosen, all T's are interpreted as U's, and if DNA is chosen, all U's are interpreted as T's.

Temperature:
The temperature is specified in degrees Celcius and is a a real number between 0 and 100. The number must be expressed using decimal notation, e.g. 37 or 15.55.

Parameters for melting temperature calculation:
For the melting temperature calculation, the user must specify whether the oligos are self-complementary at midpoint, are non-self complementary with an equimolar mixture of both types of molecule, or are non-self complementary with the concentration of Sequence 2 being much greater than that of Sequence 1. In addition, the target concentration of Sequence 1 can be specified, and also the Ionic concentration. Note that ionic concentration is currently used only in calculating the melting temperature. Calculations of enthalpy and entropy assume an ionic concentration of 1M.

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.

PairFold output:

PairFold returns three secondary structures along with the free energy, enthalpy, entropy, and melting temperature of each. If the first and second sequences are R1 and R2 respectively, then these structures are for the pairs of sequences (R1, R2), (R1, R1), and (R2, R2). (We note that since the range of pseudoknotted structures for (R1, R2) is exactly the same as for (R2, R1), there is no need to also output the minimum energy structure for (R2, R1)).

Each structure is output using dot-parenthesis notation, in which a matching pair of parentheses 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. Links are provided to the output structures in CT (Connectivity Table) and RNAML formats.

Computation time:
The CPU time used to calculate the results is presented. Our current server machine is a PC with dual Intel Xeon 2GHz CPUs with 512 KB CPU cache each, and 4GB of RAM running Redhat Linux, Version 2.4.18 SMP. To keep the load on our server manageable and response times of the online services reasonably low, we limit the length of the input sequences for the online version of PairFold to the maximal processing time to 1 hour of wall-clock time (using wall-clock time in this context means that the maximal CPU tim e available for processing the given input may be reduced when the server load is high). If the maximal processing time is exceeded, the server notifies the user that the output has not been calculated and recommends that the user try at another time.

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.