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DescriptionA base pair probability matrix that indicates the ease of secondary base energy pairing has often been used for sequence analysis of structural RNA. In recent years, it has been found that large amounts of non-protein-encoding RNAs are transcribed in higher eukaryotes, and in order to conduct sequence analysis of these RNAs, There is an increasing need for methods of determining local base pair probabilities where the distance is limited to W or less. In the past, there were only programs that used such probability calculations to use unrealistically simplified models and those that used approximate calculation methods. Rfold is the first software that can calculate local base pair probabilities without approximation based on the energy model of secondary structure. When the sequence length is N, Rfold calculates local base pair probability with the time complexity of O (NW2) and the complexity of O (N + W2) region. Furthermore, Rfold is implemented with an algorithm that predicts secondary structures based on the Maximal Expected Accuracy method, which has recently been validated.
Main Institutes of managementComputational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST)
Country of the InstituteJapan
URL of the site-
InterfaceSource code
Input exampleClick source code botton
Amount of the all data for download(Mbyte) | Method to obtain the all data.-
External resources (databases) in building the product.None
Data typeRNA
Biological species in the main concernAll species
Conditions of useAttribution&Share AlikeUser account is not required.
Frequency of updates (in last two years)1
Last date of updates (date of confirmation)2011/12/07 (2019/07/05)
Main IDs used in the productsNone
How to make a link to get access to each IDs.None
external databases to which this database/tool have linksNone
Published papers (PubMed IDs)pmid:18056736
Operational StatusClosed