The RME Server

Restrained MaxExpect Based secondary RNA structure prediction

RME introduction

A tool for RNA secondary structure prediction with multiple types of experimental probing data. It can use experimental pairing probabilities to restrain the partition function, and predict the structure with maximum restrained expected accuray based on a MEA algorithm, MaxExpect (Lu *et al*., 2009 *RNA* ). It is based on the *RNAstructure* package. It also provides preprocessing scripts for transforming the SHAPE, PARS and DMS-seq data into pairing probability according a posterior probabilistic model. Moreover, it also contains a utility for optimizing the parameters of RME by RME-Optimize.

Upload Data Files (SHAPE)

Data File Needed Valid Format Upload
The compressed data file for training (size limit:<5M) zip/tar/gz/rar/tar.gz
Sequence data for test (size limit:<1M) FASTA(.fa)
Data file containing reactivity for test (size limit:<1M) txt

Do you want to apply automatic RME-optimized?

Not use (Probably lose some details but only need 10 seconds)

Use (Automatic optimization but may cost around 15 minutes)

Advanced option for RME-Preprocess

Constant (0.535, the default setting)
The Training RNAs
Partition Function for Each RNA

Quantile Normalization (the default setting)
2%/8% Rule Normalization
No Normalization

Advanced option for RME-Prediction

(If you have already select using the automatic optimized step, then there is no need to adjust the parameters below by yourself)
1. Customize the value for parameter m (>0):

2. Customize the value for parameter gamma-1 (0~1):

3. Customize the value for parameter gamma-2 (0~1):