RNAiFold 2.0
(Synthetic RNA design)

Design synthetic functional RNA molecules in three simple steps

RNAiFold 3.0 is now available!

Rfam-based design server

Email address: (optional):

Step1
Step2
Step3

Find sequences in the seed aligment whose predicted minimum free energy structure corresponds to the alignment consensus structure

Include sequences whose minimum free energy structure IS NOT IDENTICAL to the alignment consensus structure

Use sample

Select a Rfam family Only those Rfam families which contains at least one sequence whose MFE structure is the target structure are shown. Step 2 will display only those sequences in the selected family whose MFE structure is identical to the consensus structure for the given energy model and dangling treatment.

Only those Rfam families which contains at least one sequence whose MFE structure is the target structure are shown. Step 2 will display only those sequences in the selected family whose MFE structure is identical to the consensus structure for the given energy model and dangling treatment.

Energy model
Dangling end treatment

Find compatible sequences using inverse folding

Either upload a file containing a single RNA structure, paste in an RNA structure, or fill in fields in the verbose form.

File upload Paste input Verbose input

Fill the following fields:
Fasta comment

Target structure (required) Required target structure in dot bracket notation, a comma indicates that the position may be paired or not. For hybridization of two RNA sequences an ampersand ('&') separates the two single-molecule portions of the hybridization structure.

Sequence

Use LNS		Energy model:
Temperature (ºC):		Dangling end treatment:

Base pair constraints Structure of compatible base pairs A secondary structure in dot bracket notation, solutions will be compatible with the given structure.

A secondary structure in dot bracket notation, solutions will be compatible with the given structure.

List of incompatible base pairs

Incompatible base pairs can be specified in two different formats: - Dot bracket notation: A secondary structure where paired positions are disallowed in the solution. - Base pair list: A list of base pairs or base pair ranges separated by commas. Single base pairs are represented by 2 numbers (i j) and base pair ranges by the expression (P i j k), indication that i cannot form a base pair with any position between j and j+k-1.

Amino acid constraints Target amino acid sequences List of target amino acid sequences separated by commas (no spaces). (See manual)

Expand search to similar amino acids based on

Explore sequences translated into codons that are similar to the target amino acid sequence. Similarity criteria can be: - Do not expand: Solutions must code exactly the target structure(s). - BLOSUM62 matrix based: Allow amino acids with a similarity score over a given threshold (-4 to 4) - Classification based: We propose two classifications defined in our dictionary. If specific compatible amino acid constraints provided this field does not apply.

Search maximizing blosum similarity score Instead of performing an exhaustive search try to find a sequence where the sum of amino acid similairy score is maximum. Note that the search stops when ONE optimal solution is found, the selected number of solutions have been found (even if they are not all optimal) or when the time limit is reached. This has no effect if no target amino acids sequence(s) have been provided.

Instead of performing an exhaustive search try to find a sequence where the sum of amino acid similairy score is maximum. Note that the search stops when ONE optimal solution is found, the selected number of solutions have been found (even if they are not all optimal) or when the time limit is reached. This has no effect if no target amino acids sequence(s) have been provided.

Or create your own compatibile aminoacid constraints using our dictionary

List a compatible amino acid constraints separated by commas (no spaces allowed). Limit the search space to sequences that translate into specific codons indicated by the given constraints. IUPAC codes and other symbols indicated in our dictionary are allowed. Note that specifying compatible amino acid constraints prevents expanding search from the target amino acid sequences.See manual for a detailesd explanation)

Starting positions of amino acid sequences List of starting positions (separated by commas) for the given mino acid target sequences and constraints.Starting positions are 1 by default.

List of starting positions (separated by commas) for the given mino acid target sequences and constraints.Starting positions are 1 by default.

Energy constraints

Free energy:	Min:	Max:
Free energy minimization

Nucleotide composition

GC content:

Min:

Max:

Minimum and maximum GC content between 0 and 100

Maximum consecutive nucleotides:
A:		C:		G:		U:

Limit GC pairs:	Min:	Max:
Limit AU pairs:	Min:	Max:
Limit GU pairs:	Min:	Max:

Limit A bases:	Min:	Max:
Limit C bases:	Min:	Max:
Limit G bases:	Min:	Max:
Limit U bases:	Min:	Max:

RNAiFold 2.0 (Synthetic RNA design)

Design synthetic functional RNA molecules in three simple steps

RNAiFold 3.0 is now available!

Rfam-based design server

RNAiFold 2.0
(Synthetic RNA design)