Freiburg RNA Tools
CopraRNA - sRNA Targeting
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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 format NC_XXXXXX where 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 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.

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

Input

? sRNA sequences (3-8):

? Organism of interest:

? Extract sequences around:
start codon stop codon
? nt up (1-300):
? nt down (1-300):

? Description:
? Your Email:
(optional)
(optional)

When using CopraRNA please cite :

Results are computed with CopraRNA version 1.3.0