Freiburg RNA Tools
RaSE - Help
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Introduction

RaSE uses the graph vectorization technique of EDeN to compute a score indicative of the structural stability responsibility of each nucleotide in an RNA sequence. The score is computed as the similarity of the structure obtained by changing a single nucleotide with respect to the original structure. The structure is based on RNAplfold base pair probabilities and thus reflects the overall structural ensemble accessible to the RNA molecule. Per sequence position, only the mutation that yields the largest structural difference is reported.
Results are computed with RaSE version 1.0.0 using VRNA 2.2.10 and EDeN 2.0

Overview

The following parameters are used to control the execution of RaSE

Furthermore, additional information is available

Input

?  RNA sequence

The sequence of the RNA molecule to investigate.
The parameter constraints are: String length has to be in range (10,2000). Maximally 1 line is allowed. Has to be of alphabet [ACGU]

Output

?  Mark best

Provide the minimum number of genes to be analyzed simultaneously.
The parameter constraints are: Input value has to be parsable as a Integer. The value must be greater than or equal to 1 and must be smaller than or equal to 10.

RaSE structure graph

?  Average probability cutoff

Minimal base pair probability to be incorporated in structure graph.
The parameter constraints are: Input value has to be parsable as a Double. The value must be greater than or equal to 0 and must be smaller than or equal to 1.

?  Minimal solid edge probability

Minimal base pair probability to incorporate a base pair as a solid edge within the structure graph.
The parameter constraints are: Input value has to be parsable as a Double. The value must be greater than or equal to 0 and must be smaller than or equal to 1.

?  Minimal number of edges per node

Maximal number of edges connected to a nucleotide node within the structure graph.
The parameter constraints are: Input value has to be parsable as a Integer. The value must be greater than or equal to 1 and must be smaller than or equal to 100.

RNAplfold

?  Window size

Length of the windows used to compute base pairing probabilities.
The parameter constraints are: Input value has to be parsable as a Integer. The value must be greater than or equal to 10 and must be smaller than or equal to 2000.

?  Maximal base pair span

Maximal length/span of base pairs considered for base pairing probabilities.
The parameter constraints are: Input value has to be parsable as a Integer. The value must be greater than or equal to 10 and must be smaller than or equal to 2000.

?  No lonely base pairs

Whether or not lonely base pairs are allowed for base pair probability computations.
The parameter constraints are: Input value has to be parsable as a Boolean.

EDeN

?  Complexity of features

Complexity of EDeN graph features.
The parameter constraints are: Input value has to be parsable as a Integer. The value must be greater than or equal to 1 and must be smaller than or equal to 20.

?  Bit size for feature encoding

Bit size to encode graph features.
The parameter constraints are: Input value has to be parsable as a Integer. The value must be greater than or equal to 8 and must be smaller than or equal to 32.

Output Description

RaSe outputs a space separated tabular file with the following format: the first line contains the Minimum Free Energy structure (MFE) in dot-bracket notation of the original sequence; the following lines contain the nucleotide (nt) position, the nt one letter code (A|C|G|U), the nt code for the mutation that most changes the computed structure, the similarity score between the original structure and the structure obtained by the mutation, the MFE structure of the mutated sequence in dotbracket notation and an optional character * marking the top dissimilar cases.

             (((((((((((.((.......)).))))..............((((((...))))))(((((.......)))))))))))).
  0 G C 0.63 ((((.((((((.((.......)).)))))).)))).......((((((...))))))(((((.......)))))........ 
  1 C G 0.23 (((((((.((((((((.........((((((.......))))))..))))))))...(((((.......)))))))))))). *

The structure image depicts the graph encoding of the most probable RNA structure: edges representing the backbone or base pairs with a probability higher than --hard_threshold are displayed with a solid line, edges between base pairs with probability in the interval --avg_bp_prob_cutoff and --hard_threshold are displayed with a dashed line. The node label is composed of the original nt (above) and the mutation that most changes the computed structure (below). The color intensity is proportional to 1 - similarity, so that darker nodes are the ones that have the largest effect on the structure.

The plot image depicts the nt position on the top x axis, the original nt on the bottom x axis, the mutation that most changes the computed structure on the bottom x axis but inside the plot, the score = 1 - similarity on the y axis, so that the highest bar corresponds to the mutation that has the largest effect on the structure.

The structures image depicts the graph encoding of the individual k mutations that most changes the computed structure. The title associated with each graph is composed of the original nt, the position and the mutation that most changes the computed structure. The node color encode the different nts (A|C|G|U). The line encoding is the same as for the structure plot (see above).

RaSE exposes several library functions that can be used inside other projects. See examples of use in the Jupyter notebook

List of Changes