Select a function. [?]

Select a software.


Input RNA sequences.

RNA sequences (Multi-FASTA format)

File upload
Dot Bracket Structure
Folded RNA Sequence
Parameter settings.

Name Value Description
max_time set maximal time <float> in minutes for each pairwise alignment.
time_factor set scale factor <float> for internal time estimation.
Name Value Description
SCSLENGTH set length of stem candidates <2-4>
BASEPROBTHRESHOLD set threshold of base pairing probability <0.001-1>
BASEPAIRSCORECONST set control parameter of the prediction of base pairs <1-10>
Name Value Description
Stem Fragment Length word length in stem candidate.
Name Value Description
Local (option L) execute local alignment.
Cost (option C) cost table to be used.
Name Value Description
Gap open penalty Specifies the gap-open score of affine gap as negative real value.
Gap extend penalty Specifies the gap-extend score of affine gap as negative real value less than or equal to gap-open penalty.
Allow to insert base pairs Enables to insert any base pairs which are not in the folded sequence. (It is not recommendable, because the scores for inserting base pairs are not defined.)
Score matrix Proposed by Gorodkin or by Klein is available.
Indespensable parameter
Name Value Description
Minimum support
number >= 1 (integer)
 minimum support of derived pattern. support is defined by (number of sequences containing this pattern)/(number of input sequences).
Maximum cost of pattern maximum cost of pattern. Generally pattern with small const is more reliable than pattern with large cost.

Optional parameter