Freiburg RNA Tools
CopraRNA - sRNA Targeting
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IFF
CopraRNA

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, MicA, MicC, MicF, OxyS, RprA, RybB, RyhB, SgrS, Spot42, and for Non-enteric bacteria: FsrA, LhrA2, PrrF1, SR1, IhtA.

Note, in contrast to this server, the stand-alone CopraRNA software does not limit the problem size, provides enhanced functionality, and offers a batch processing-friendly command line interface. For this reasons, you might consider to install CopraRNA locally

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

Try CopraRNA with this example: 5 ChiX sequences (~2h) (input|result) ?

Sequence input

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? Organism of interest:

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? Description:
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When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.4 using IntaRNA 2.4.1