nocoRNAc (non-coding RNA characterization) is a Java program for the prediction and characterization of ncRNA transcripts in bacteria. nocoRNAc takes the coordinates of putative ncRNA loci as input and annotates them with transcriptional features to conduct strand-specific transcript predictions. Our approach is not limited to intergenic regions but also applied to predict cis-encoded asRNA transcripts.
For the detection of the transcript’s 3′ end nocoRNAc integrates the program TransTermHP (Kingsford et al., 2007) to predict Rho-independent terminator signals. The 5′ start is predicted by the detection of destabilized regions in the genomic DNA. For this purpose we implemented the so-called SIDD model (Benham, Bi, 2004), which has been shown to be applicable to the detection of promoter regions in microbial genomes. Therefore, nocoRNAc does not have to rely on information about known TFBS. The putative transcriptional features are then combined to classify ncRNA loci into either being an ncRNA transcript or not. For ncRNAs that are classified as transcripts the strand is automatically specified, and its boundaries are derived from the SIDD sites and the Rho-independent transcription termination signal.
Those loci that are classified not to be a transcript might be false positive predictions or they contain cis-regulatory motifs. For the latter, nocoRNAc incorporates other functionalities for the further analysis of the ncRNA loci such as the search for known RNA motifs from the Rfam database.
Furthermore, nocoRNAc provides methods for the prediction of RNA-RNA interactions between ncRNAs and mRNAs. All results can be studied in detail in nocoRNAc‘s integrated interactive R environment.

Citation

If you use nocoRNAc, please cite:

nocoRNAc: Characterization of non-coding RNAs in prokaryotes
Alexander Herbig, Kay Nieselt
BMC Bioinformatics 2011, 12:40 (31 January 2011)

Download

nocoRNAc is free for academic use.
The latest version of nocoRNAc (v1.23 – December 06, 2011) can be downloaded from here.
nocoRNAc’s User Guide can be downloaded from here.
Example data for S. coelicolor can be downloaded from here.

Requirements

For some functionalities nocoRNAc utilizes external programs, which are listed in the following. The source code has to be retrieved from the respective websites and the compiled binaries and other files needed can be placed in nocoRNAc’s progs folder.

For detailed instructions, please have a look at section 5 (Integrated Programs) of the User Guide.

TransTermHP is used to detect Rho-independent transcription terminators:
TransTermHP – http://transterm.cbcb.umd.edu/

Erpin and CMsearch are used to search the Rfam database:
Erpin – http://rna.igmors.u-psud.fr/Software/erpin.php
CMsearch – http://infernal.janelia.org/

IntaRNA is used for RNA-RNA interaction prediction:
IntaRNA – http://www.bioinf.uni-freiburg.de/Software/

To use the interactive R environment R has to be installed:
http://www.r-project.org/

In addition the Biostrings package from Bioconductor is needed:
http://www.bioconductor.org/

Contact

For questions and bug reports please contact Kay Nieselt.