@Article{Backofen:Hess:Compu_predi_sRNAs:2010,
  author =	 {Backofen, Rolf and Hess, Wolfgang R.},
  title =	 {Computational prediction of {sRNAs} and their targets in 
                  bacteria},
  journal =	 {RNA Biol},
  year =	 {2010},
  issn =         {1555-8584},
  issn =         {1547-6286},
  volume =	 {7},
  number =	 {1},
  pages =	 {33-42},
  user =	 {arichter},
  pmid =	 {20061798},
  abstract =	 {There is probably no major adaptive response in bacteria 
                  which does not have at least one small RNA (sRNA) as part of 
                  its regulatory network controlling gene expression. Thus, 
                  prokaryotic genomes encode dozens to hundreds of these 
                  riboregulators. Whereas the identification of putative sRNA 
                  genes during initial genome annotation is not yet common 
                  practice, their prediction can be done subsequently by 
                  various methods and with variable efficacy, frequently 
                  relying on comparative genome analysis. A large number of 
                  these sRNAs interact with their mRNA targets by antisense 
                  mechanisms. Yet, the computational identification of these 
                  targets appears to be challenging because frequently the 
                  partial and incomplete sequence complementarity is difficult 
                  to evaluate. Here we review the computational approaches for 
                  detecting bacterial sRNA genes and their targets, and 
                  discuss the current and future challenges that this exciting 
                  field of research is facing.}
}