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.
