rPredictor

Introduction

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rPredictor is a project dedicated to ribosomal RNA (rRNA) secondary structure research. The two main contributions of rPredictor are:

  • The rPredictor infrastructure: a website, database and toolkit for search and prediction
  • CP-predict: a new secondary structure prediction algorithm specifically for ribosomal RNA

The project was partially supported by grant no. 550214 of the Charles University Grant Agency (GAUK).

Goals of rPredictor

The aim of rPredictor is twofold. We develop and deploy a technique of predicting ribosomal RNA secondary structure and make the resulting structural information readily available. At the same time, the rPredictor database contains rich annotations of rRNA structures and the underlying sequences, providing an unified interface for rRNA research for both academics and professionals outside academia.

A secondary goal of rPredictor is extensibility: it should be easy to integrate third-party tools.

Motivation

Gene translation is the process of implementation of genetic information, which forms a living organism. The unit central to translation is the ribosome.

The “scaffold” (and major part) of the ribosome consists of ribosomal ribonucleic acids (rRNA), which are critical for its function. Because the function of biological molecules is mostly determined by their spatial structure, understanding the role of rRNA in translation depends on understanding rRNA structures. While rRNA nucleotide sequences can be obtained relatively easily, determining their three-dimensional structure is very demanding: sequences are known for hundreds of eucaryotic organisms while spatial structures only for about 5.

Secondary structures are an intermediate step between sequences and three-dimensional structures. Understanding secondary structures enables at least partial study of rRNA behavior, and secondary structures can be predicted from sequences (to a much greater extent than the spatial structures). However, ribosomal RNA are notoriously hard problems for secondary structure prediction.

In recent years, improved imaging methods have led to detailed measurement of spatial structures of the ribosome in a few organisms (and a secondary structure can be derived from these measurements). The availability of these structures, together with a high degree of conservation in the ribosome, should make it possible to derive secondary structures for other ribosomal RNA as well.

While the importance of ribosomes and ribosomal RNA has been recognized for several decades, support for bioinformatical work over the available ribosomal data is fragmented and unsatisfactory. Various sites dedicated to rRNA exist: most notably the SILVA database and the Comparative RNA Website (CRW). However, none of them are satisfactory: the CRW site is hard to navigate, fails to provide crucial information (e.g. origin of provided secondary structure) and does not support mass retrieval; SILVA has no support for structural bioinformatics. The rPredictor infrastructure aims to overcome the shortcomings of these sites and make working with rRNA as easy as possible.

rPredictor components

The rPredictor infrastructure has several key components:

  • a database of rRNA sequences and secondary structures (rData) and Extraction-Transformation-Load mechanisms to build rData (rETL),
  • a set of tools that perform standard tasks on the data like similarity search or secondary structure prediction (rTools),
  • a new algorithm dedicated to rRNA secondary structure prediction (CP-predict),
  • an internet portal and back-end that makes the rData and rTools components accessible to the research community and general public (rWeb),
  • documentation, including relevant scientific literature (rDoc)

The rPredictor infrastructure is built and maintained by the rPredictor student team from the Computer Science branch of the Faculty of Mathematics and Physics, Charles University, Prague. (Contact us here.)

What now?

To start using the rPredictor website right away, go search or predict.

If you wish to read more about rPredictor:

Table Of Contents

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1. rPredictor User Documentation

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