NanoFolder Help Page
OverviewNanoFolder is a program for predicting the secondary structure of one or multiple RNA sequences including pseudoknots. The usage is straightforward: after pasting the sequence(s) in FASTA format text field named "Sequence Data" one can click "submit" at the bottom of the page. For sequences greater 100 nucleotides, it is recommended to save the provided job ID, in order to be able to access the status of the job submission. This can be accomplished by bookmarking the web page that appears after job submission. Once the computation is finished, the predicted secondary structure is displayed in two different text formats ("bracket-notation" as well as "CT-format") as well as a secondary structure image.
ExamplesA list of available examples of RNA sequences can be found here.
Input Format FASTAThe FASTA format contains alternating the names of sequences (preceded by a > character) and the sequence data (both "ACGU" alphabet and "ACGT" alphabet are accepted by the server).
Output format: circle diagramThe circle diagram was created using the Circos software. The basic idea is that the RNA sequences are represented as segments (arcs) of a circle (5' to 3' strand orientations correspond to a clock-wise directionality). Predicted base pairs are represented as lines connecting the corresponding base pairing residues. Intra-strand base pairs are depicted as blue connecting lines, inter-strand base pairs are depicted as red connecting lines. The nucleotide identity and residue indices are shown at the circle perimeter.
Output format: bracket notationThe bracket notation is a character string that has a length equal to the number of residues of the sequence. Each character of the bracket notation indicates the base pairing status of the corresponding residue (for example the first character of the brackent notation describes the base pairing of the first residue of the sequence). Base pairs are indicated by opening and closing parenthesis or by capital letters. Residues that do not participate in base pairing are denoted by a hyphen.
Output format: CT formatThe CT format lists in separate rows the base nucleotide sequence as well as their base pairing status. The first column contains the residue number, the second column contains the residue symbol (A,C,G or U). The fifth column contains either zero or the residue number of a base pairing residue.
ApproachThe NanoFolder program was developed in order to facilitate the prediction of RNA secondary structures (using one or multiple sequences) without restricting the complexity of considered pseudoknot interactions. Allowing all pseudoknots can be accomplished by making a list of complementary sequence fragments (corresponding to potential helices) and having an algorithm that decides which helices to choose for the predicted structure. NanoFolder places an internally generated list of potential RNA helices in the order of their free energy contributions. This approach is well suited to RNA sequences with long helices or whose concatenated secondary structure corresponds to non-nested base pairs. Furthermore, it is currently one of the few programs, that performs an RNA secondary structure prediction for the simultaneous folding of a multitude of sequences.
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