title: Systematic identification of stem-loop containing sequence families in bacterial genomes.
abstract: BACKGROUND
  Analysis of non-coding sequences in several bacterial genomes brought to the identification of families of repeated sequences, able to fold as secondary structures. These sequences have often been claimed to be transcribed and fulfill a functional role. A previous systematic analysis of a representative set of 40 bacterial genomes produced a large collection of sequences, potentially able to fold as stem-loop structures (SLS). Computational analysis of these sequences was carried out by searching for families of repetitive nucleic acid elements sharing a common secondary structure.
  
  
  RESULTS
  The initial clustering procedure identified clusters of similar sequences in 29 genomes, corresponding to about 1% of the whole population. Sequences selected in this way have a substantially higher aptitude to fold into a stable secondary structure than the initial set. Removal of redundancies and regrouping of the selected sequences resulted in a final set of 92 families, defined by HMM analysis. 25 of them include all well-known SLS containing repeats and others reported in literature, but not analyzed in detail. The remaining 67 families have not been previously described. Two thirds of the families share a common predicted secondary structure and are located within intergenic regions.
  
  
  CONCLUSIONS
  Systematic analysis of 40 bacterial genomes revealed a large number of repeated sequence families, including known and novel ones. Their predicted structure and genomic location suggest that, even in compact bacterial genomes, a relatively large fraction of the genome consists of non-protein-coding sequences, possibly functioning at the RNA level.
authors.affiliation: CEINGE Biotecnologie Avanzate scarl, Via Comunale Margherita 482, 80145 Napoli, Italy. cozzuto@ceinge.unina.it
authors.forename: Luca
authors.initials: L
authors.lastname: Cozzuto
authors.forename: Mauro
authors.initials: M
authors.lastname: Petrillo
authors.forename: Giustina
authors.initials: G
authors.lastname: Silvestro
authors.forename: Pier Paolo
authors.initials: PP
authors.lastname: Di Nocera
authors.forename: Giovanni
authors.initials: G
authors.lastname: Paolella
mesh_terms: D001483:Base Sequence; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics*; D016680:Genome, Bacterial; D008390:Markov Chains; D008957:Models, Genetic; D005810:Multigene Family; D009690:Nucleic Acid Conformation; D012091:Repetitive Sequences, Nucleic Acid; D016415:Sequence Alignment
chemical_list: D004269:DNA, Bacterial