Assume we identify - by RNA-seq, tiling arrays, by prediction - possible candidate regions for non-coding, small RNAs. I wish to verify and predict the function of as many RNAs as possible by computation before going to the lab. One could use eg. Rfam to find similar sequences, after that we are left with more than 90% that have no match. One could predict the 2D structure using eg. RNAfold, compare that using RNAforester. But that does not get me even close to a function prediction. Do you have experience with other tools or a better computational pipeline that gets more information out of the ncRNA candidates, possibly even something specific to bacteria.
How are you doing your comparison to Rfam? If you're just running rfam_scan.pl or the CMs then this may not give you the results you really want. See the recent paper by Kolbe & Eddy to hear more about the limitations of CMs on truncated sequences. Could explain some of your lack of sensitivity vs Rfam. However there is a terrifying number of ncRNAs not yet covered by Rfam.