Freiburg RNA Tools
CopraRNA - sRNA Targeting
BIF
IFF

CopraRNA - sRNA Targeting

CopraRNA is a tool for sRNA target prediction. It computes whole genome predictions by combination of distinct whole genome IntaRNA predictions. As input, CopraRNA requires at least 3 homologous sRNA sequences from 3 distinct organisms in FASTA format. Furthermore each organisms' genome has to be part of the NCBI Reference Sequence (RefSeq) database (i.e. it should have exactly this NZ_* or this NC_XXXXXX format where * stands for any character and X stands for a digit between 0 and 9). Depending on sequence length (target and sRNA), amount of input organisms and genome sizes, CopraRNA can take up to 24h or longer to compute (in most cases it is significantly faster). It is suggested you supply your email and return when the job has finished. As output, CopraRNA produces a CopraRNA p-value sorted list of putative targets. Results can be viewed in the browser, but closer examination of the downloadable data is suggested.

Precomputed results for Enterobacteria: ArcZ, ChiX, CyaR, DsrA, FnrS, GcvB, GlmZ, MicA, MicC, MicF, OmrA, OmrB, OxyS, RprA, RybB, RyhB, SgrS, Spot42, and for Non-enteric bacteria: FsrA, LhrA2, PrrF1, SR1, IhtA.

For papers describing the tool refer to the reference section below. Please cite us when using our tools.
For more information check the help page.

The CopraRNA webserver is currently offline for maintenance from 20/04/2015 to 26/04/2015.

Due to current connectivity issues between the University of Freiburg and the NCBI servers, we have temporarily deactivated CopraRNA. We will restart the service as soon as possible.

We apologize for the inconvenience.

When using CopraRNA please cite :

Results are computed with CopraRNA version 2.0.2