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VfoldMCPX Web Server Help
About VfoldMCPX
Restrictions
Input parameters
Result page
Check existing jobs
About VfoldMCPX
VfoldMCPX is a physics-based model for predicting 2D structures and folding thermodynamics of multistrand RNA complexes, with and without pseudoknots. The model employs a partition function-based algorithm and the Vfold-derived loop entropic parameters, and can predict secondary structural motifs and tertiary motifs such as H-type pseudoknots.
VfoldMCPX web server provides a web interface to predict 2D structures and base pairing probabilities of RNA multistrand complexes, using the VfoldMCPX model.
Restrictions
To avoid long computational time, we restrict the total sequence length, the strand length, the temperature, and the number of strands as follows.
(1) Total sequence length:
- ≤300 nt for predicting structures without crossing base pairs.
- ≤180 nt for predicting structures with H-type pseudoknots and for the specific strand order.
- ≤150 nt for predicting structures with H-type pseudoknots and for all the strand combinations.
(2) Number of strands:
≤9 strands for the specific strand order.- ≤5 strands for all the strand combinations.
(3) Length of each strand: ≥ 3 nt.
(4) Temperature: 0 °C to 200 °C.
Input parameters
(0) Number of strands
Number of RNA strands. You can specify a number between 2 and 9 (inclusive). Please click the "confirm" button or press the Enter key to confirm the number.
(1) Temperature
Set the temperature for the prediction (default value is 37 °C). You can specify a number between 0 and 200 (inclusive).
(2) Energy parameters for base stacks
Set the base stacking energy parameters (including mismatched base stacks), either from Turner’s parameters (default) or from the MFOLD parameter set.
(3) Enter sequences (strands)
Our web server recognizes A, a, C, c, G, g, U and u. Your input strands will be transformed to a full RNA sequence using a three-nucleotide linker marked as ”XXX”.
(4) Job name
Set the job name. Note that job ID is not the job name. A job ID contains the job name you provide and a 4-letter unique code randomly generated by our server. You can find the job ID after submitting the job.
(5) Your email address
Optional. To receive the results by email, please select the checkbox and enter a valid address. You will receive the results by email, if provided.
(6) Pseudoknots
You can specify the type of the structures included in the prediction: no pseudoknots are allowed (default) or H-type pseudoknots are allowed to form. Note that it is not guaranteed that pseudoknots are always predicted (e.g., for short sequences).
(7) Strand order
Your can specify the strand order in the prediction: user-defined strand order (default, from RNA 1 to RNA N) or all the strand combinations (all the different sequential orders of the strands will be enumerated).
Result page
After submitting the job, you will be redirected to a page displaying the job information. You can bookmark the page, save the job ID to check the job status. The page will be refreshed automatically and will display the results once the computation is finished.
Once you receive the result page, you can find:
(1) Top predictions: Top unique structures among the secondary structure ensemble, visualized by the VARNA applet.
(2) List of predicted structures: A set of structures ranked by the free energies.
(3) Predicted base pairing probabilities: Base pairing probabilities for the full sequence (transformed from the input strands). Note that you won't receive the file if you select "all the strand combinations" for the strand order option.
Check existing jobs
You can search for the results of existing (finished or in process) jobs using job ID on the VfoldMCPX home page. A job ID contains the job name you provide and a 4-letter unique code randomly generated by our server.
The expiration time for finished jobs is 3 months. Please download the files you want to keep on your local computer.
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