# Limitations of the RNAstructure Web Servers

The RNAstructure Web Servers have certain limitations on the input that can be given to them. These limitations are in place for web use only, so they do not apply to any of the downloadable software on the Mathews Lab homepage.

Interface | Limit |
---|---|

AllSub | Sequence must be no longer than 2500 nucleotides. |

bifold |
Sequence 1 must be no longer than 250 nucleotides.
Sequence 2 must be no longer than 250 nucleotides. |

Bimolecular Secondary Structure (Predict a Bimolecular Secondary Structure) |
Sequence 1 must be no longer than 200 nucleotides.
Sequence 2 must be no longer than 75 nucleotides. |

bipartition |
Sequence 1 must be no longer than 250 nucleotides.
Sequence 2 must be no longer than 250 nucleotides. |

DuplexFold |
Sequence 1 must be no longer than 10000 nucleotides.
Sequence 2 must be no longer than 75 nucleotides. |

Dynalign |
Sequence 1 must be no longer than 500 nucleotides.
Sequence 2 must be no longer than 500 nucleotides. |

EnsembleEnergy | Sequence must be no longer than 2500 nucleotides. |

Fold | Sequence must be no longer than 4000 nucleotides. |

MaxExpect | Sequence must be no longer than 4000 nucleotides. |

Multilign |
A maximum of 10 sequences can be used.
Each sequence must be no longer than 600 nucleotides. |

Multiple Sequence Secondary Structure (Predict a Secondary Structure Common to Three or More Sequences) |
A maximum of 10 sequences can be used.
Each sequence must be no longer than 600 nucleotides. |

Paired Secondary Structure (Predict a Secondary Structure Common to Two Sequences) |
Sequence 1 must be no longer than 500 nucleotides.
Sequence 2 must be no longer than 500 nucleotides. |

partition | Sequence must be no longer than 4000 nucleotides. |

PARTS |
Sequence 1 must be no longer than 500 nucleotides.
Sequence 2 must be no longer than 500 nucleotides. |

ProbablePair | Sequence must be no longer than 4000 nucleotides. |

ProbKnot | Sequence must be no longer than 4000 nucleotides. |

Single Sequence Secondary Structure (Predict a Secondary Structure) |
Sequence must be no longer than 4000 nucleotides. |

stochastic | Sequence must be no longer than 4000 nucleotides. |

TurboFold |
A maximum of 12 sequences can be used.
Each sequence must be no longer than 2500 nucleotides. |