About

The rboAnalyzer is a tool for analysis of BLAST output when the query sequence is an RNA. It is designed to work with ncRNAs and other RNA sequences that have functional structure.

The rboAnalyzer process requested high-scoring pairs (HSPs) in BLAST output and extends the subject sequence matches to their full length. Then estimates homology of the full-length matches. And finally predicts secondary structures of the full-length matches by multiple methods.

The rboAnalyzer was originally developed as command-line application which is accessible from github.com/cas-bioinf/rboAnalyzer.

Used rboAnalyzer pipeline backend version is 0.1.5a1.

This is a webserver frontend to rboAnalyzer which can analyze BLAST outputs from NCBI BLAST webserver.

The webserver is able to process blastn searches in nucleotide databases with indexed by sequences identifiers (accessions) referring to GenBank or RefSeq accessions format (ncbi.nlm.nih.gov/Sequin/acc.html), provided that the accessions are available.

Citation

Marek Schwarz, Jiří Vohradský, Josef Pánek, rboAnalyzer webserver: web service for non-coding RNA characterization from NCBI BLAST output, Bioinformatics, 2021; https://doi.org/10.1093/bioinformatics/btab073

Acknowledgements

rboAnalyzer webserver was developed at Jiri Vohradsky's group Laboratory of Bioinformatics Institute of Microbiology of the CAS.

The development was supported by:

• This work was supported by ELIXIR CZ research infrastructure project (MEYS Grant No: LM2015047) including access to computing and storage facilities.
• This work was supported from European Regional Development Fund - Project "ELIXIR-CZ: Budování kapacit" (No. CZ.02.1.01/0.0/0.0/16_013/0001777).
• This work was also supported by Czech Science Foundation GA15-00885S.