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.
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
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
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.
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.
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.