4. The rPredictor Toolkit Reference

Herein lies a complete description of the input fields for each tool in the rPredictor toolkit (rTools).

Each input field is described with a short table:

Input type A description of what input the field expects
Modifiers A list of possible modifiers (see below)
Multipliers The type and cardinality of possible multipliers (see below)

Modifiers are extra options like “greater than” or “before” that modify the meaning of the input to the given field.

Multipliers enable multiple inputs to be given to the field, for example to search for sequences with one of accession numbers from some group. The type of a multiplier is either OR, which says “Find me records that match at least one of my criteria”, or AND, which says “Find me only records that match all of my criteria”. For example, the Length field has AND multiplier: the sequence must fulfill all length constraints placed upon it.

The cardinality of a multiplier says how many inputs you can at most give for the multiplied field. For instance, the Accession number field has a cardinality of 10, so ten different accession numbers can be searched for.

Modifiers and multipliers can be combined - for instance, an interval can be specified by combining a two-valued “before” and “after” modifier with an AND type multiplier (this is the case in First published).

4.4. CP-predict2

A short description of what CP-predict2 does is here: CP-predict2

A detailed description is here: CP-predict: a two-phase algorithm for rRNA structure prediction

4.4.1. FASTA header

Input type String
Modifiers  
Multipliers  

The FASTA header containing the name under which the sequence should be kept during prediction. Currently, the only way Cp-predict uses the header is in the output.

4.4.2. Sequence

Input type String (allowed characters: A, C, G, T, U, M, R, W, S, Y, K, V, H, D, B, N)
Modifiers  
Multipliers  

The Sequence input field expects a DNA or RNA sequence. Wildcards (M, R, W, S, Y, K, V, H, D, B, N) will be replaced with the most probable possibility and the resulting sequence will be passed to the prediction algorithm.

Note

10 sequences can be predicted at one time.

4.4.3. Template

Input type Select (automatic, 1C2X, 4V6X - B2, etc.)
Modifiers  
Multipliers  

A template that should be used for the prediction (see CP-predict: a two-phase algorithm for rRNA structure prediction). The exact list of possible values is extracted at the time of loading the webpage according to the current templates in the rData. In the case of ‘automatic’ option, each query sequence is globally aligned with all templates and a template from the most probable alignment is used for the prediction.

4.4.4. z-score

Input type Checkbox
Modifiers  
Multipliers  

Whether to compute the probability of the predicted structure.

Note

Computing z-score will noticeably slow down the prediction as it requires generate and predict random sequences.