Identification of small non-coding RNAs in bacterial genome annotation using databases and computational approaches

Abstract

RNA genes are unquestionable today, non-coding RNA is functional but its classification at the present is complex due to lack of computational tools. The vast progress in computer science for DNA and protein is not enough to resolve folding and function of RNA. Fortunately, computational tools for solving RNA concerns are in progress: web source as Centroid Homofold, CentroidFold (CBRC), Rfam (Sanger-HHMI, Janelia farm), sRNAdb (MGIL), RNApredator (Vienna RNA web server), TargetRNA2 (Wellesley College), Noncoding RNAdatabase (IBC), Mfold (CAS) and RNAcon (IMTC) are quickly supplying the bioinformatics gaps. In this work was used those tools to fill and appoint the intergenic annotation in the Leuconostoc mesenteroides bacterium, recently sequenced in 454 Roche. More than 2000 intergenic sequence were run on the mentioned tools. Various ncRNA were classified as Mir-(#)s, many T-Boxes, various L(#) leaders and some ones TPPs, yybp-ykoY and ykkC-yxkD, between others. Other interesting structures without matching in Rfam, ncRNA databases were annotated as hypothetical ncRNA. © Springer International Publishing Switzerland 2014.