RNA Designer input:
Structure to be designed, in dot-bracket format:
Desired secondary structure, from 5' to 3'.
Unpaired base positions are represented by ".", and paired
base positions are represented by "(" and ")".
To keep the load on our server manageable, the length
of the structure is restricted to 500 bases or less.
Constraints on bases for individual sequence positions.
If sequence constraints are used, a string
of the same length as the desired secondary structure
needs to be specified, using IUPAC nucleotide symbols
(A,C,G,U,T for positions in which the respective
base must appear; R, Y for positions in which
A or G, C or U/T can appear; and N or - for positions
in which any base can be used).
If no sequence constraint string is specified,
it is assumed that any base can occur in any position
of the desired structure.
Sequence constraints are always strictly enforced.
Desired folding temperature, i.e., the temperature at which
the result sequence is predicted to have the specified
secondary structure as its minimal free energy structure.
The temperature is specified in degrees Celsius and is a real number
between 0 and 100. The number must be expressed using decimal notation,
e.g. 37 or 15.55.
Number of sequences to design:
The number of sequences that are to be designed.
For values > 1, each sequence is designed in an independent
run of the algorithm, using the same parameters,
except for the random number seed.
If a random number seed r is specified,
the first sequence is designed using seed r,
the next using r+1, etc.
In the output, the designed sequences are sorted
according to the thermodynamic energy of their respective
predicted MFE structure.
Target GC content for paired/unpaired regions:
These parameters can be used to control the target GC content of paired / unpaired
bases in the desired structure, and are specified as percentages.
In our current implementation,
these parameters represent a probabilistic bias
towards the desired GC content in the search process. In cases,
where many sequences exist for a given structure (or substructure),
the output sequences can be expected to match the specified target GC content
quite closely; in cases where finding a correctly folding sequence with
the target GC content is hard or impossible, the search is allowed to
drift from the GC target.
Random number seed:
Optional parameter that represents the integer value used for initialising
the random number generator. By specifying a seed value,
the design process becomes completely deterministic
and reproducible. If no value is specified,
a value is derived from the system time on our server
is used, and can be expected to be different for any two
runs. In either case, the actual seed value used for each run
is reported as part of the ouput, and can be used to reproduce that
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 receive the output via email.
RNA Designer output:
Sequence n and MFE structure:
Sequence found by RNA designer and corresponding minimal free energy structure
as predicted by the Vienna folding algorithm at the specified temperature.
Each result sequence and its predicted MFE structure can also
be accessed in CT (Connectivity Table) and RNAML format.
If multiple sequences were designed, these are listed in order
of increasing minimal free energy values of the predicted MFE structure.
Distance to desired structure:
Number of bases in the output sequence that are not paired (or unpaired)
in the output secondary structure as specified in the input secondary structure.
A value of O indicates that the predicted secondary structure
of the result sequence precisely matches the desired secondary structure.
Minimum free energy:
Free energy of the predicted structure in kcal/mol, as computed by the Vienna RNA
Package RNAfold algorithm.
Probability of MFE in ensemble:
Probability of the minimal free energy structure in the thermodynamic
ensemble, as calculated by the Vienna RNA Package partition function
Actual GC content of paired/unpaired regions:
Actual percentage of G and C bases within the set of
paired/unpaired positions in the designed sequence.
This may vary from the specified target GC content values,
particularly in cases where there are few
sequences that are predicted into the desired structure.
Total time required for obtaining the reported RNA Designer result on our server.
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.
Identifier of the query - this is primarily used for maintainance and
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.