Identified families,out of ,are predicted by RNAz to share a typical secondary structure. This group consists of wellknown intergenic families,like the E. coli PUBIME and ERIC repeats,and their homologues in other species,as well as many less recognized families,the majority of which described in isolated reports,but not characterized in detail (see Table. Practically all intergenic repeats,previously shown or predicted to fold into a RNA secondary structure,have been discovered. The only exceptions are the S. pneumoniae RUP as well as the R. conorii RPE repeats,which,although identified by the pipeline,usually do not fall into this group,since RNAz could not predict a shared secondary structure better than the defined threshold. For recognized families,the sequence TCS-OX2-29 boundaries,as predicted by the pipeline,are essentially coincident with those previously reported in literature. Distinct discrepancies were discovered only in two families. Inside the N. meningitidis NEMIS elements,the present search identified the central bp core,but failed to extend the similarity to either the partial or the full bp repeats described by Mazzone et al. . Similarly,for the S. pneumoniae RUP household,only bases were detected out of your complete bp components .Known and novel households In nicely characterized genomes,like those of enterobacteria,practically all recognized households have been detected,as well as a handful of new ones. In E. coli,the identified PUBIME,ERIC and BoxC families were recognized and feature shared secondary structures,when the only new one particular identified,the Eco household,is predicted as unable to fold. PUBIME repeats were also detected in S. typhi as two related variants (a complete size in addition to a shorter 1,only the former predicted to fold) and in S. typhimurium,as well as two novel families,Sal and Sal (Table. For each of themPage of(web page number not for citation purposes)BMC Genomics ,:biomedcentralFigure Schematic representation on the general process Schematic representation on the overall procedure.Page of(web page number not for citation purposes)BMC Genomics ,:biomedcentralRNAz could predict a shared secondary structure of the complex sort. As anticipated,ERIC sequences had been detected not simply in E. coli,but also in Y. pestis and V. cholerae : Y. pestis repeats are predicted to fold with a structure closely equivalent towards the E. coli elements. In contrast,ERIC sequences detected in V. cholerae are certainly not predicted to fold,becoming bp shorter than both E. coli and Y. pestis homologues,as a result of selective erosion of their TIRs. Yersiniae ERIC sequences have already been shown to regulate the degree of expression of neighboring genes by folding into RNA harpins . V. cholerae ERIC,becoming unable to fold,could thus not function as RNA stability determinants. Most potentially structured new households have been found in species much less analyzed experimentally or whose genome was much more lately sequenced,like pseudomonaceae,bordetellae,mycobacteria. For both novel and identified families,the predicted widespread secondary structure is usually a stemloop (see Sta and ERIC in Figure. Within a fraction of circumstances,nevertheless,RNAz evaluation proposes different structures. Some households function a double hairpin (see EFA and Pae in Figure and others feature a complicated structure containing a SLS (not shown).Genomic localization Genomic localization highlights the preferential tendency of PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/18276852 repeated sequences with a predicted popular secondary structure to lie within intergenic regions; this really is accurate for each identified and novel ones. In contrast,households found within.