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Updated: Nov 19, 2025

A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

Published on: December 2, 2009

rboAnalyzer webserver: web service for non-coding RNA characterization from NCBI BLAST output.

Marek Schwarz¹, Jiří Vohradský¹, Josef Pánek¹

¹Laboratory of Bioinformatics, Institute of Microbiology, The Czech Academy of Sciences, Praha, Czech Republic.

Bioinformatics (Oxford, England)

|February 1, 2021

Summary

This study introduces rboAnalyzer, a web service for better characterization of non-coding RNAs (ncRNAs). It extends sequence data from BLAST outputs to predict homology and secondary structures, aiding RNA analysis.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

NCBI BLAST is a common tool for sequence alignment.
Characterizing non-coding RNAs (ncRNAs) can be challenging with standard BLAST outputs.
High-scoring pairs (HSPs) in BLAST may contain uncharacterized RNA sequences.

Purpose of the Study:

To develop a web service for enhanced characterization of ncRNAs.
To improve the analysis of subject sequences from NCBI BLAST outputs.
To provide tools for predicting RNA homology and secondary structures.

Main Methods:

The rboAnalyzer web service is based on a command-line application.
It extends subject sequences within selected HSPs to their full length.
Predicts homology and secondary structures of these extended sequences.

Main Results:

The web service facilitates the characterization of previously unannotated ncRNAs in BLAST results.
It offers interactive analysis with search, filtering, and data export functionalities.
Improves the usability and depth of analysis for RNA sequences.

Conclusions:

rboAnalyzer provides a valuable web service for improving ncRNA characterization.
The tool aids researchers in understanding RNA function and structure from BLAST data.
Offers an easy-to-use, interactive platform for bioinformatics analysis.