About this service |
This is an RNA fold server. It takes an alignment of RNA sequences as input and predicts a common structure for all sequences. The algorithm is described in the references below.
This service has just been made available. Comments are appreciated.
Insert your sequences in fasta format in the box below. An example of the fasta format is shown in the box. At the moment, the server has a maximum of 40 sequences, and an alignment length of 500.
The accepted nucleotide symbols are: 'A', 'B', 'C', 'D', 'G', 'K', 'M', 'N', 'R', 'S', 'T', 'U', 'V', 'W', 'X' and 'Y', as used in the extended nucleotide alphabet. Gap signs, '-', are also accepted along with the above letters in lower case.
Bjarne Knudsen (bk@daimi.au.dk)
Sequence form |
When you press `Fold RNA' your data will be processed.
Known structure can be incorporated by including a sequence called 'structure'. The structure is indicated in three ways:
- By parentheses. Columns with matching parentheses are forced to pair with each other
- Using 's'. Columns with an 's' will be forced to be single stranded.
- Using 'd'. Columns with a 'd' will be forced to pair with another column.
All symbols different from the above means that nothing is assumed about the structure of that position. An example. Notice that some structures are impossible and may yield strange results (e.g. all positions paired and loops of size less than three).
References |
- Knudsen, B. and J. J. Hein (1999) Using stochastic context free grammars and molecular evolution to predict RNA secondary structure. Bioinformatics, 15 (6), 446-454.
- Knudsen, B. and Hein, J. (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Research, 31 (13), 3423-3428
